R/metric_values.R
In leppott/BioMonTools: Tools for Biomonitoring and Bioassessment
Defines functions
metric.values.coral
metric.values.algae
metric.values.fish
metric.values.bugs
metric.values
Documented in
metric.values
metric.values.algae
metric.values.bugs
metric.values.coral
metric.values.fish
#' @title Calculate metric values
#'
#' @description This function calculates metric values for bugs, fish, algae
#' , and coral. Inputs are a data frame with SampleID and taxa with phylogenetic
#' and autecological information (see below for required fields by community).
#' The dplyr package is used to generate the metric values.
#'
#' @details All percent metric results are 0-100.
#'
#' No manipulations of the taxa are performed by this routine.
#' All benthic macroinvertebrate taxa should be identified to the appropriate
#' operational taxonomic unit (OTU).
#'
#' Any non-count taxa should be identified in the "Exclude" field as "TRUE".
#' These taxa will be excluded from taxa richness metrics (but will count for
#' all others).
#'
#' Any non-target taxa should be identified in the "NonTarget"
#' field as "TRUE". Non-target taxa are those that are not part of your
#' intended #' capture list; e.g., fish, herps, water column taxa, or water
#' surface taxa in a benthic sample. The target list will vary by program. The
#' non-target taxa will be removed prior to any calculations.
#'
#' Excluded taxa are ambiguous taxa (on a sample basis), i.e.,
#' the parent taxa when child taxa are present. For example, the parent taxa
#' Chironomidae would be excluded when the child taxa Tanytarsini is present.
#' Both would be excluded when Tanytarsus is present. The markExcluded function
#' can be used to populated this field.
#'
#' There are a number of required fields (see below) for metric to calculation.
#' If any fields are missing the user will be prompted as to which are missing
#' and if the user wants to continue or quit. If the user continues the missing
#' fields will be added but will be filled with zero or NA (as appropriate).
#' Any metrics based on the missing fields will not be valid.
#'
#' A future update may turn these fields into function parameters. This would
#' allow the user to tweak the function inputs to match their data rather than
#' having to update their data to match the function.
#'
#' Required fields, all communities:
#'
#' * SAMPLEID (character or number, must be unique)
#'
#' * TAXAID (character or number, must be unique)
#'
#' * N_TAXA
#'
#' * INDEX_NAME
#'
#' * INDEX_CLASS (BCG or MMI site category; e.g., for BCG PacNW valid values
#' are "hi" or "lo")
#'
#' Additional Required fields, bugs:
#'
#' * EXCLUDE (valid values are TRUE and FALSE)
#'
#' * NONTARGET (valid values are TRUE and FALSE)
#'
#' * PHYLUM, SUBPHYLUM, CLASS, SUBCLASS, INFRAORDER, ORDER, FAMILY, SUBFAMILY,
#' TRIBE, GENUS
#'
#' * FFG, HABIT, LIFE_CYCLE, TOLVAL, BCG_ATTR, THERMAL_INDICATOR, FFG2, TOLVAL2,
#' LONGLIVED, NOTEWORTHY, HABITAT, UFC, ELEVATION_ATTR, GRADIENT_ATTR,
#' WSAREA_ATTR, HABSTRUCT
#'
#' Additional Required fields, fish:
#'
#' * N_ANOMALIES
#'
#' * SAMP_BIOMASS (biomass total for sample, funciton uses max in case entered
#' for all taxa in sample)
#'
#' * NATIVE: NATIVE or other text values
#'
#' * DA_MI2, SAMP_WIDTH_M, SAMP_LENGTH_M, , TYPE, TOLER, TROPHIC, SILT,
#' FAMILY, GENUS, HYBRID, BCG_ATTR, THERMAL_INDICATOR, ELEVATION_ATTR,
#' GRADIENT_ATTR, WSAREA_ATTR, REPRODUCTION, HABITAT, CONNECTIVITY, SCC
#'
#' Additional Required fields, algae:
#'
#' * EXCLUDE, NONTARGET, PHYLUM, ORDER, FAMILY, GENUS, BC_USGS, TROPHIC_USGS,
#' SAP_USGS, PT_USGS, O_USGS, SALINITY_USGS, BAHLS_USGS, P_USGS, N_USGS,
#' HABITAT_USGS, N_FIXER_USGS, MOTILITY_USGS, SIZE_USGS, HABIT_USGS,
#' MOTILE2_USGS, TOLVAL, DIATOM_ISA, DIAT_CL, POLL_TOL, BEN_SES, DIATAS_TP,
#' DIATAS_TN, DIAT_COND, DIAT_CA, MOTILITY, NF
#'
#' Valid values for fields:
#'
#' * FFG: CG, CF, PR, SC, SH
#'
#' * HABIT: BU, CB, CN, SP, SW
#'
#' * LIFE_CYCLE: UNI, SEMI, MULTI
#'
#' * THERMAL_INDICATOR: STENOC, COLD, COOL, WARM, STENOW, EURYTHERMAL
#' , COWA, NA
#'
#' * LONGLIVED: TRUE, FALSE
#'
#' * NOTEWORTHY: TRUE, FALSE
#'
#' * HABITAT: BRAC, DEPO, GENE, HEAD, RHEO, RIVE, SPEC, UNKN
#'
#' * UFC: integers 1:6 (taxonomic uncertainty frequency class)
#'
#' * ELEVATION_ATTR: LOW, HIGH
#'
#' * GRADIENT_ATTR: LOW, MOD, HIGH
#'
#' * WSAREA_ATTR: SMALL, MEDIUM, LARGE, XLARGE
#'
#' * REPRODUCTION: BROADCASTER, SIMPLE NEST, COMPLEX NEST, BEARER, MIGRATORY
#'
#' * CONNECTIVITY: TRUE, FALSE
#'
#' * SCC (Species of Conservation Concern): TRUE, FALSE
#'
#' 'Columns to keep' are additional fields in the input file that the user wants
#' retained in the output. Fields need to be those that are unique per sample
#' and not associated with the taxa. For example, the fields used in
#' qc.check(); Area_mi2, SurfaceArea, Density_m2, and Density_ft2.
#'
#' If fun.MetricNames is provided only those metrics will be returned in the
#' provided order. This variable can be used to sort the metrics per the user's
#' preferences. By default the metric names will be returned in the groupings
#' that were used for calculation.
#'
#' The fields TOLVAL2 and FFG2 are provided to allow the user to calculate
#' metrics based on alternative scenarios. For example, including both HBI and
#' NCBI where the NCBI uses a different set of tolerance values (TOLVAL2).
#'
#' If TAXAID is 'NONE' and N_TAXA is '0' then metrics **will** be calculated
#' with that record. Other values for TAXAID with N_TAXA = 0 will be removed
#' before calculations.
#'
#' For 'Oligochete' metrics either Class or Subclass is required for
#' calculation.
#'
#' The parameter boo.Shiny can be set to TRUE when accessing this function in
#' Shiny. Normally the QC check for required fields is interactive. Setting
#' boo.Shiny to TRUE will always continue. The default is FALSE.
#'
#' The parameter 'taxaid_dni' denotes taxa to be included in Do Not Include
#' (DNI) metrics but dropped from all other metrics. Only for benthic metrics.
#'
#' Breaking change from 0.5 to 0.6 with change from Index_Name to Index_Class.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @param fun.DF Data frame of taxa (list required fields)
#' @param fun.Community Community name for which to calculate metric values
#' (bugs, fish, algae, or coral)
#' @param fun.MetricNames Optional vector of metric names to be returned.
#' If none are supplied then all will be returned. Default=NULL
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param fun.cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
# @param MetricSort How metric names should be sort; NA = as is, AZ =
# alphabetical. Default = NULL.
#' @param boo.marine Should estuary/marine metrics be included.
#' Ignored if fun.MetricNames is not null. Default = FALSE.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#' @param metric_subset Subset of metrics to be generated. Internal function.
#' Default = NULL
#' @param taxaid_dni Taxa names to be included in DNI (Do Not Include) metrics
#' (n = 3) but dropped for all other metrics. Only for benthic metrics.
#' Default = NULL
#'
#' @return data frame of SampleID and metric values
#'
#' @examples
#' # Example 1, data already in R
#'
#' df_metric_values_bugs <- metric.values(data_benthos_PacNW, "bugs")
#'
#' \dontrun{
#' # View Results
#' View(df_metric_values_bugs)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 2, data from Excel
#'\dontrun{
#' # Packages
#' library(readxl)
#' library(reshape2)
#'
#' df_samps_bugs <- read_excel(system.file("extdata/Data_Benthos.xlsx"
#' , package = "BioMonTools")
#' , guess_max = 10^6)
#'
#' # Columns to keep
#' myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")
#'
#' # Run Function
#' df_metric_values_bugs <- metric.values(df_samps_bugs[1:100, ]
#' , "bugs"
#' , fun.cols2keep = myCols)
#'
#' # View Results
#' View(df_metric_values_bugs)
#' }
#'
#' # Get data in long format so can QC results more easily
#' df_long <- melt(df_metric_values_bugs, id.vars = c("SAMPLEID"
#' , "INDEX_NAME"
#' , "INDEX_CLASS"
#' , toupper(myCols))
#' , variable.name = "METRIC_NAME"
#' , value.name = "METRIC_VALUE")
#'
#'\dontrun{
#' # Save Results
#' write.table(df_long, file.path(tempdir(), "metric.values.tsv")
#' , col.names = TRUE, row.names = FALSE, sep = "\t")
#'
#' # DataExplorer Report
#' library(DataExplorer)
#' create_report(df_metric_values_bugs
#' , output_file = file.path(tempdir()
#' , "DataExplorer_Report_MetricValues.html"))
#' create_report(df_samps_bugs
#' , output_file = file.path(tempdir()
#' , "DataExplorer_Report_BugSamples.html"))
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 3, specific metrics or metrics in a specific order
#' ## reuse df_samps_bugs from above
#'
#' # metric names to keep (in this order)
#' myMetrics <- c("ni_total", "nt_EPT", "nt_Ephem", "pi_tv_intol", "pi_Ephem"
#' , "nt_ffg_scrap", "pi_habit_climb")
#'
#' # Run Function
#' df_metric_values_bugs_myMetrics <- metric.values(df_samps_bugs, "bugs"
#' , fun.MetricNames = myMetrics)
#'\dontrun{
#' # View Results
#' View(df_metric_values_bugs_myMetrics)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 4, fish metrics
#'
#' df_metric_values_fish <- metric.values(data_fish_MBSS, "fish")
#'
#'\dontrun{
#' # View Results
#' View(df_metric_values_fish)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 5, periphyton (algae) metrics
#'
#' # df_metric_values_periphyton <- metric.values(data_diatom_mmi_dev, "algae")
#'
#'\dontrun{
#' # View Results
# # View(df_metric_values_periphyton)
#' }
#'
# #~~~~~~~~~~~~~~~~~~~~~~~
# # INDIANA BCG
#
# library(readxl)
# library(reshape2)
#
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_Indiana.xlsx"
# , package="BCGcalc"), sheet="R_Input")
# dim(df.samps.bugs)
# # rename some fields
# names(df.samps.bugs)
# names(df.samps.bugs)[names(df.samps.bugs)=="VisitNum"] <- "SampleID"
# names(df.samps.bugs)[names(df.samps.bugs)=="FinalID"] <- "TaxaID"
# names(df.samps.bugs)[names(df.samps.bugs)=="Count"] <- "N_Taxa"
# # Add field
# df.samps.bugs[, "INDEX_NAME"] <- "BCG.IN"
# #
# # Run Function
# myDF <- df.samps.bugs
# df.metric.values.bugs <- metric.values(myDF, "bugs")
#
# # View Results
# View(df.metric.values.bugs)
#
# # Get data in long format so can QC results more easily
# df.long <- melt(df.metric.values.bugs, id.vars=c("SAMPLEID"
# , "INDEX_NAME"
# , "INDEX_CLASS")
# , variable.name="METRIC_NAME"
# , value.name="METRIC_VALUE")
# # Save Results
# write.table(df.long, "metric.values.tsv", col.names=TRUE, row.names=FALSE
# , sep="\t")
#
# # DataExplorer Report
# library(DataExplorer)
# create_report(df.metric.values.bugs, "DataExplorer_Report_MetricValues.html")
# create_report(df.samps.bugs, "DataExplorer_Report_BugSamples.html")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# QC 20180319
#
# library(readxl)
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_PacNW.xlsx"
# , package="BCGcalc"))
# fun.DF <- df.samps.bugs
# # PREP
# fun.DF <- as.data.frame(fun.DF)
# names(fun.DF) <- toupper(names(fun.DF))
# fun.DF <- fun.DF[fun.DF[,"N_TAXA"]>0, ]
# fun.DF <- fun.DF[fun.DF[,"NONTARGET"]==FALSE,]
# fun.DF[,"INDEX_CLASS"] <- toupper(fun.DF[,"INDEX_CLASS"])
# #
# myDF <- fun.DF
# #
# # Convert values to upper case (FFG, Habit, Life_Cycle)
# myDF[, "HABIT"] <- toupper(myDF[, "HABIT"])
# myDF[, "FFG"] <- toupper(myDF[, "FFG"])
# myDF[, "LIFE_CYCLE"] <- toupper(myDF[, "LIFE_CYCLE"])
# myDF[, "THERMAL_INDICATOR"] <- toupper(myDF[, "THERMAL_INDICATOR"])
# # Add extra columns for FFG and Habit
# # (need unique values for functions in summarise)
# # each will be TRUE or FALSE
# myDF[, "HABIT_BU"] <- grepl("BU", myDF[, "HABIT"])
# myDF[, "HABIT_CB"] <- grepl("CB", myDF[, "HABIT"])
# myDF[, "HABIT_CN"] <- grepl("CN", myDF[, "HABIT"])
# myDF[, "HABIT_SP"] <- grepl("SP", myDF[, "HABIT"])
# myDF[, "HABIT_SW"] <- grepl("SW", myDF[, "HABIT"])
# myDF[, "FFG_COL"] <- grepl("CG", myDF[, "FFG"])
# myDF[, "FFG_FIL"] <- grepl("CF", myDF[, "FFG"])
# myDF[, "FFG_PRE"] <- grepl("PR", myDF[, "FFG"])
# myDF[, "FFG_SCR"] <- grepl("SC", myDF[, "FFG"])
# myDF[, "FFG_SHR"] <- grepl("SH", myDF[, "FFG"])
# myDF[, "LC_MULTI"] <- grepl("MULTI", myDF[, "LIFE_CYCLE"])
# myDF[, "LC_SEMI"] <- grepl("SEMI", myDF[, "LIFE_CYCLE"])
# myDF[, "LC_UNI"] <- grepl("UNI", myDF[, "LIFE_CYCLE"])
# myDF[, "TI_COLD"] <- grepl("COLD", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_COLDCOOL"] <- grepl("COLD_COOL", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_COOLWARM"] <- grepl("COOL_WARM", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_WARM"] <- grepl("WARM", myDF[, "THERMAL_INDICATOR"])
# #
# `%>%` <- dplyr::`%>%`
# mySamp <- "06039CSR_Bug_2006-07-13_0"
# x <- dplyr::filter(myDF, SAMPLEID==mySamp)
# # 26 taxa
# x <- dplyr::filter(myDF, SAMPLEID==mySamp, (BCG_ATTR == "4" | BCG_ATTR == "5"
# | BCG_ATTR == "6"))
# # 22 taxa (good)
# x <- dplyr::filter(myDF, SAMPLEID==mySamp
# , (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# , (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# , (is.na(GENUS) == TRUE | GENUS!="Juga")
# , (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")
# )
# # filter works here
# # 5 taxa and 202 ind.
#
# met.val <- dplyr::summarise(dplyr::group_by(x, SAMPLEID, INDEX_NAME, INDEX_CLASS)
# # individuals #
# , ni_total=sum(N_TAXA)
# #
# , nt_NonInsArachDecaClump_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
# & (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# & (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# & (is.na(GENUS) == TRUE | GENUS!="Juga")
# & (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")]
# , na.rm = TRUE)
# #
# , pi_NonInsArachDecaClump_BCG_att456 = sum(N_TAXA[
# (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# & (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# & (is.na(GENUS) == TRUE | GENUS!="Juga")
# & (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")]
# , na.rm = TRUE)
# )
# View(met.val)
#
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# DomN metric
# library(readxl)
# library(dplyr)
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_PacNW.xlsx"
# , package="BCGcalc"))
# myDF <- as.data.frame(df.samps.bugs)
# names(myDF) <- toupper(names(myDF))
#
#
# # arrang in descending order (SampleID and N_Taxa)
# x <- myDF %>% arrange(SampleID, desc(N_Taxa))
# #y <- x %>% top_n(2, wt=N_Taxa) # only gets 2 rows on entire DF
# y <- x %>% group_by(SampleID) %>% filter(row_number()<=5)
# a <- table(y$SampleID)
#
# X <- myDF %>% arrange(SampleID, desc(N_Taxa)) %>%
# group_by(SampleID) %>%
# filter(row_number()<=5)
# A <- table(X$SampleID)
# View(A)
#
# # then Sum N_Taxa by SampleID
#
# # too many results (i.e., those with ties)
# z <- myDF %>% group_by(SampleID) %>% top_n(5, N_Taxa)
# View(z)
# table(z$SampID)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# OLD, Remove
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# # Metrics, MBSS Index, Fish
# myIndex <- "MBSS.2005.Fish"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Fish <- as.character(droplevels(unique(
# thresh[thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Fish <- taxa_fish
# myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish)
# View(myMetric.Values.Fish)
#
# # Metrics, Index, Benthic Macroinvertebrates, genus
# # (generate values then scores)
# myIndex <- "MBSS.2005.Bugs"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Bugs.MBSS <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Bugs.MBSS <- taxa_bugs_genus
# myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs", myMetrics.Bugs.MBSS)
# View(myMetric.Values.Bugs.MBSS)
#
# # Metrics, MSW Index, Benthic Macroinvertebrates, family
# myIndex <- "MSW.1999.Bugs"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Bugs.MSW <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Bugs.MSW <- taxa_bugs_family
# myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs", myMetrics.Bugs.MSW)
# View(myMetric.Values.Bugs.MSW)
#~~~~~~~~~~~~~~~~~~~~~~~~~~
# # QC
# ## Fish
# myIndex <- "MBSS.2005.Fish"
# thresh <- metrics_scoring
# (myMetrics.Fish <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# myDF <- myDF.Fish
# myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish, TRUE)
# fun.DF <- myDF.Fish
# fun.SampID <- "SampleID"
# fun.Community <- "fish"
# fun.MetricNames <- myMetrics.Fish"
#~~~~~~
# fun.DF <- df_samps_bugs
# fun.Community <- "bugs"
# fun.MetricNames <- c("nt_total", "nt_EPT")
# boo.Adjust <- FALSE
# fun.cols2keep=NULL
# MetricNames <- fun.MetricNames
# cols2keep <- fun.cols2keep
#~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @export
metric.values <- function(fun.DF
, fun.Community
, fun.MetricNames = NULL
, boo.Adjust = FALSE
, fun.cols2keep = NULL
, boo.marine = FALSE
, boo.Shiny = FALSE
, verbose = FALSE
, metric_subset = NULL
, taxaid_dni = NULL) {
boo_debug_main <- FALSE
debug_main_num <- 0
debug_main_num_total <- 7
boo_QC <- FALSE
# QC
if (boo_QC) {
fun.DF <- data_benthos_PacNW#[, 1:32] # 598, 37
#fun.DF <- data_benthos_MBSS # 5066, 37
fun.Community <- "bugs"
fun.MetricNames <- NULL
boo.Adjust <- FALSE
fun.cols2keep <- NULL
boo.marine <- FALSE
boo.Shiny <- FALSE
verbose <- TRUE
metric_subset <- NULL
taxaid_dni <- NULL
# Create DNI sample
taxaid_dni <- "DNI"
fun.DF <- rbind(fun.DF, fun.DF[1, ])
fun.DF[nrow(fun.DF), "TaxaID"] <- taxaid_dni
tail(fun.DF)
}## boo_QC
# global variable bindings
N_TAXA <- TAXAID <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# Munge ####
if (verbose == TRUE) {
debug_topic <- "munge"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Data Munging (common to all data types)
# Convert to data.frame. Code breaks if fun.DF is a tibble.
fun.DF <- as.data.frame(fun.DF)
# convert Field Names to UPPER CASE
names(fun.DF) <- toupper(names(fun.DF))
# convert cols2keep to UPPER CASE
if (!is.null(fun.cols2keep)) {
#names(fun.cols2keep) <- toupper(fun.cols2keep)
fun.cols2keep <- toupper(fun.cols2keep)
}##IF~!is.null(fun.cols2keep)~END
# subset to upper case
if (!is.null(metric_subset)) {
metric_subset <- toupper(metric_subset)
} else {
metric_subset <- "ALL"
}##IF~!is.null(metric_subset)~END
metric_subset <- ifelse(is.na(metric_subset), NA, toupper(metric_subset))
# QC, missing cols ----
# bare minimum, applies to all communities
if (verbose == TRUE) {
debug_topic <- "QC missing cols"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ boo_debug_main
#QC, Add required fields for this part of the code
if (toupper(fun.Community) == "CORAL") {
col.req <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS")
} else {
col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "INDEX_NAME", "INDEX_CLASS")
} # end if/else
col.req.missing <- col.req[!(col.req %in% toupper(names(fun.DF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0 & interactive() == TRUE) {
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
# special condition for Shiny
# Shiny counts as interactive()==TRUE but cannot access this prompt in Shiny.
if (boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n")
, sep = "\n"))
}##IF.user.input.END
# Add missing fields
if (verbose == TRUE) {
debug_topic <- "add missing fields"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
## Add missing, Index_Name
req.name <- "INDEX_NAME"
if (req.name %in% col.req.missing) {
fun.DF[, req.name] <- "BioMonTools"
}## IF ~ req.name
## Add missing, INDEX_CLASS
req.name <- "INDEX_CLASS"
if (req.name %in% col.req.missing) {
fun.DF[, req.name] <- fun.Community
}## IF ~ req.name
## Add missing, N_Taxa
req.name <- c("SAMPLEID", "TAXAID", "N_TAXA")
if (sum(req.name %in% col.req.missing) == length(req.name)) {
req.name.missing <- req.name[req.name %in% col.req.missing]
stop(paste("Required columns missing: "
, paste(paste0(" ",req.name.missing), collapse = "\n"),sep = "\n"))
}## IF ~ req.name
## old
#fun.DF[,col.req.missing] <- NA_character_
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames:"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(fun.DF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
# Remove Count = 0 taxa unless TaxaID = NONE
if (verbose == TRUE) {
debug_topic <- "remove count 0"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
#fun.DF <- fun.DF[fun.DF[,"N_TAXA"]>0, ]
if (toupper(fun.Community) != "CORAL") {
fun.DF <- fun.DF %>% dplyr::filter(N_TAXA > 0 | TAXAID == "NONE")
}## IF ~ taxa not zero
# non-target taxa removed in community function, if appropriate
#
# SiteType to upper case
if (verbose == TRUE) {
debug_topic <- "sitetype toupper"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# fun.DF[,"INDEX_CLASS"] <- toupper(fun.DF[,"INDEX_CLASS"])
# convert community to upper case
fun.Community <- toupper(fun.Community)
# run the proper sub function
if (verbose == TRUE) {
debug_topic <- "start subfunctions"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Subfunctions ----
# Run subfunction based on community
if (fun.Community == "BUGS") {##IF.START
metric.values.bugs(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.marine = boo.marine
, boo.Shiny = boo.Shiny
, verbose = verbose
, metric_subset = metric_subset
, taxaid_dni = taxaid_dni)
} else if (fun.Community == "FISH") {
metric.values.fish(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, boo.Shiny = boo.Shiny
, verbose = verbose)
} else if (fun.Community == "ALGAE") {
metric.values.algae(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.Shiny = boo.Shiny
, verbose = verbose)
} else if (fun.Community == "CORAL") {
metric.values.coral(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.Shiny = boo.Shiny
, verbose = verbose)
}##IF.END
}##FUNCTION.metric.values.START
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Bugs
#'
#' @description Subfunction of metric.values for use with Benthic
#' Macroinvertebrates
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.marine Should estuary/marine metrics be included.
#' Ignored if fun.MetricNames is not null. Default = FALSE.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#' @param metric_subset Subset of metrics to be generated. Internal function.
#' Default = NULL
#' @param taxaid_dni Taxa names to be included in DNI (Do Not Include) metrics
#' (n = 3) but dropped for all other metrics. Only for benthic metrics.
#' Default = NULL
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.bugs <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.marine = FALSE
, boo.Shiny
, verbose
, metric_subset
, taxaid_dni = NULL) {
#
# QC
boo_QC <- FALSE
if (boo_QC) {
myDF <- fun.DF
boo.Adjust <- boo.Adjust
cols2keep <- fun.cols2keep
MetricSort <- NA
boo.marine <- boo.marine
boo.Shiny <- boo.Shiny
verbose <- verbose
metric_subset <- NULL
taxaid_dni <- "DNI" #added last entry in previous function
}## IF ~ boo_QC
time_start <- Sys.time()
# not carrying over from previous?!
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "BUGS"
boo_debug_bugs <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 18
# global variable bindings ----
INDEX_NAME <- INDEX_CLASS <- SAMPLEID <- TAXAID <- N_TAXA <- EXCLUDE <-
BCG_ATTR <- NONTARGET <- LONGLIVED <- NOTEWORTHY <- TOLVAL <- TOLVAL2 <-
UFC <- ELEVATION_ATTR <- GRADIENT_ATTR <- WSAREA_ATTR <- NULL
FFG2_PRE <- TI_CORECOLD <- TI_COLD <- TI_COOL <- TI_WARM <- TI_NA <-
TI_CORECOLD_COLD <- TI_COOL_WARM <- NULL
PHYLUM <- SUBPHYLUM <- CLASS <- SUBCLASS <- INFRAORDER <- ORDER <-
FAMILY <- SUBFAMILY <- TRIBE <- GENUS <- NULL
FFG_COL <- FFG_FIL <- FFG_PRE <- FFG_SCR <- FFG_SHR <- FFG_MAH <- FFG_PIH <-
FFG_XYL <- FFG_OMN <- FFG_PAR <- HABITAT_SPEC <- HABITAT_UNKN <- NULL
ni_total <- ni_Americo <- ni_Gnorimo <- ni_EPT <- ni_Trich <- nt_Amph <-
nt_total <- nt_Bival <- nt_Coleo <- nt_COET <- nt_Deca <- nt_Dipt <-
nt_Ephem <- nt_EPT <- nt_ET <- nt_Gast <- nt_Insect <- nt_Isop <- nt_Mega <-
nt_NonIns <- nt_Nudib <- nt_Odon <- nt_OET <- nt_Oligo <- nt_Pleco <-
nt_POET <- nt_Poly <- nt_PolyNoSpion <- nt_Spion <- nt_Trich <- ni_Chiro <-
nt_Chiro <- nt_NonInsArachDeca_BCG_att456 <-
nt_NonInsArachDecaJugaRiss_BCG_att456 <- ni_dom02_NoJugaRiss_BCG_att456 <-
nt_NonIns_BCG_att456 <- nt_NonInsJugaRiss_BCG_att456 <- nt_BCG_att1m <-
nt_BCG_att12 <- nt_BCG_att1i2 <- nt_BCG_att123 <- nt_BCG_att1i23 <-
nt_BCG_att2 <- nt_BCG_att23 <- nt_BCG_att234 <- nt_BCG_att3 <-
nt_BCG_att4 <- nt_BCG_att45 <- nt_BCG_att5 <- nt_BCG_att56 <- nt_BCG_att6 <-
nt_BCG_attNA <- nt_EPT_BCG_att123 <- nt_ti_c <- nt_ti_cc <- nt_ti_cw <-
nt_ti_w <- nt_tv_intol <- nt_tv_intol4 <- nt_tv_toler <- nt_tv_ntol <-
nt_tv_stol <- nt_ffg_col <- nt_ffg_filt <- nt_ffg_pred <- nt_habitat_brac <-
nt_habitat_depo <- nt_habitat_gene <- nt_habitat_head <- nt_habitat_rheo <-
nt_habitat_rive <- nt_habitat_spec <- nt_habitat_unkn <- nt_BCG_att1 <-
nt_BCG_att1i <- HABITAT_BRAC <- HABITAT_DEPO <- HABITAT_GENE <-
HABITAT_HEAD <- HABITAT_RHEO <- HABITAT_RIVE <- HABIT_BU <- HABIT_CB <-
HABIT_CN <- HABIT_SP <- HABIT_SW <- LC_MULTI <- LC_SEMI <- LC_UNI <-
ni_dom02 <- ni_dom03 <- ni_dom04 <- ni_dom05 <- ni_dom06 <- ni_dom07 <-
ni_dom08 <- ni_dom09 <- ni_dom10 <- nt_ffg_scrap <- nt_ffg_shred <-
nt_habit_burrow <- nt_habit_climb <- nt_habit_cling <- nt_habit_sprawl <-
nt_habit_swim <- nt_volt_multi <- nt_volt_semi <- nt_volt_uni <- x_Shan_e <-
NULL
nt_ffg_mah <- nt_ffg_pih <- nt_ffg_xyl <- nt_ffg_omn <- nt_ffg_par <-
pi_ffg_mah <- pi_ffg_pih <- pi_ffg_xyl <- pi_ffg_omn <- pi_ffg_par <-
pt_ffg_mah <- pt_ffg_pih <- pt_ffg_xyl <- pt_ffg_omn <- pt_ffg_par <- NULL
nt_ECT <- pi_ECT <- pt_ECT <- NULL
WSAREA_S <- WSAREA_M <- WSAREA_L <- WSAREA_XL <- NULL
ELEVATION_HIGH <- ELEVATION_LOW <- GRADIENT_HIGH <- GRADIENT_LOW <-
GRADIENT_MOD <- TI_EURY <- nt_BCG_att456 <- nt_EPT_BCG_att1i23 <-
nt_NonInsTrombJuga_BCG_att456 <- nt_Tromb <- nt_ti_cold <- nt_ti_cool <-
nt_ti_cool_warm <- nt_ti_corecold <- nt_ti_corecold_cold <- nt_ti_eury <-
nt_ti_na <- nt_ti_warm <- NULL
HABSTRUCT <- HABSTRUCT_CS <- HABSTRUCT_NF <- HABSTRUCT_RM <- HABSTRUCT_SG <-
nt_Hempit <- pi_Hemipt <- pt_Hemipt <- nt_oneind <- NULL
nt_BCG_att4b <- pi_BCG_att4b <- pt_BCG_att4b <- nt_BCG_att1i234b5 <-
pi_BCG_att1i234b5 <- pt_BCG_att1i234b5 <- nt_BCG_att1i234w5 <-
pi_BCG_att1i234w5 <- pt_BCG_att1i234w5 <- NULL
nt_Hemipt <- nt_dni <- pi_dni <- pt_dni <- NULL
pi_EphemNoBaeTri <- nt_EphemNoBaeTri <- nt_COETNoBraBaeHydTri <- x_BCICTQa <-
NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC----
## QC, Missing Cols ----
if (verbose == TRUE) {
debug_topic <- "QC, missing cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
, "PHYLUM", "SUBPHYLUM", "CLASS", "SUBCLASS", "INFRAORDER"
, "ORDER", "FAMILY", "SUBFAMILY", "TRIBE", "GENUS"
, "FFG", "HABIT", "LIFE_CYCLE"
, "BCG_ATTR", "THERMAL_INDICATOR"
, "FFG2", "HABITAT", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR", "HABSTRUCT"
, "BCG_ATTR2")
col.req_logical <- c("EXCLUDE", "NONTARGET"
, "LONGLIVED", "NOTEWORTHY", "AIRBREATHER")
col.req_numeric <- c("N_TAXA", "TOLVAL", "TOLVAL2", "UFC")
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
# col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "EXCLUDE", "INDEX_NAME"
# , "INDEX_CLASS", "NONTARGET", "PHYLUM", "SUBPHYLUM", "CLASS"
# , "SUBCLASS", "INFRAORDER", "ORDER", "FAMILY", "SUBFAMILY"
# , "TRIBE", "GENUS", "FFG", "HABIT", "LIFE_CYCLE", "TOLVAL"
# , "BCG_ATTR", "THERMAL_INDICATOR", "LONGLIVED", "NOTEWORTHY"
# , "FFG2", "TOLVAL2", "HABITAT", "UFC", "ELEVATION_ATTR"
# , "GRADIENT_ATTR", "WSAREA_ATTR")
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
col.req.missing_char <- col.req_character[!(col.req_character %in% toupper(names(myDF)))]
col.req.missing_log <- col.req_logical[!(col.req_logical %in% toupper(names(myDF)))]
col.req.missing_num <- col.req_numeric[!(col.req_numeric %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
num.col.req.missing_char <- length(col.req.missing_char)
num.col.req.missing_log <- length(col.req.missing_log)
num.col.req.missing_num <- length(col.req.missing_num)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {
# Create prompt for missing columns
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
#user.input <- readline(prompt=myPrompt)
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive & boo.Shiny
# # special condition for Shiny
# # Shiny counts as interactive()==TRUE locally
# but cannot access this prompt in Shiny.
# if (boo.Shiny==FALSE) {
# user.input <- utils::menu(c("YES", "NO"), title=myPrompt)
# } else {
# message(myPrompt)
# message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
# user.input <- 1
# }## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
#myDF[, col.req.missing] <- NA
if (num.col.req.missing_char > 0) {
myDF[, col.req.missing_char] <- NA_character_
}
if (num.col.req.missing_log > 0) {
myDF[, col.req.missing_log] <- NA
}
if (num.col.req.missing_num > 0) {
myDF[, col.req.missing_num] <- NA_real_
}
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing)
, collapse = "\n")
, sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(myDF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Exclude"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "EXCLUDE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {
warning("EXCLUDE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, NonTarget----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, NonTarget"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "NONTARGET"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
NonTarget.F <- sum(myDF$NONTARGET == FALSE, na.rm = TRUE)
if (NonTarget.F == 0) {
warning("NONTARGET column does not have any FALSE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, TolVal----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, TolVal"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "TOLVAL"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
TolVal_Char_NA <- myDF[, "TOLVAL"] == "NA"
# Fails with mix of NA and "NA", rework
TolVal_Char_NA <- TolVal_Char_NA == TRUE & !is.na(TolVal_Char_NA)
if (sum(TolVal_Char_NA, na.rm = TRUE) > 0) {
#myDF[TolVal_Char_NA, "TOLVAL"] <- NA
myDF[, "TOLVAL"] <- as.numeric(myDF[, "TOLVAL"])
# will give a warning - NAs introduced by coercion
msg <- "Updated col class; TOLVAL to numeric"
message(msg)
}##IF ~ TOLVAL ~ END
## QC, TolVal2----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, TolVal2"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "TOLVAL2"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
TolVal2_Char_NA <- myDF[, "TOLVAL2"] == "NA"
if (sum(TolVal2_Char_NA, na.rm = TRUE) > 0) {
myDF[TolVal2_Char_NA, "TOLVAL2"] <- NA
myDF[, "TOLVAL2"] <- as.numeric(myDF[, "TOLVAL2"])
msg <- "Updated col class; TOLVAL2 to numeric"
message(msg)
}##IF ~ TOLVAL2 ~ END
## QC, UFC----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, UFC"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "UFC"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
UFC_Char_NA <- myDF[, "UFC"] == "NA"
if (sum(UFC_Char_NA, na.rm = TRUE) > 0) {
myDF[UFC_Char_NA, "UFC"] <- NA
myDF[, "UFC"] <- as.numeric(myDF[, "UFC"])
msg <- "Updated col class; UFC to numeric"
message(msg)
}##IF ~ UFC ~ END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging ####
if (verbose == TRUE) {
debug_topic <- "Munging"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Remove NonTarget Taxa (added back 20200715, missing since 20200224)
# Function fails if all NA (e.g., column was missing) (20200724)
if (verbose == TRUE) {
debug_topic <- "Munging, NonTarget"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "NONTARGET"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
myDF <- dplyr::filter(myDF, NONTARGET != TRUE | is.na(NONTARGET))
# # Convert columns to upper case (Phylo, FFG, Habit, Life_Cycle)
if (verbose == TRUE) {
debug_topic <- "Munging, text cols, toupper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# col2upper <- c("TAXAID", "PHYLUM", "SUBPHYLUM", "CLASS", "SUBCLASS"
# , "INFRAORDER", "ORDER", "FAMILY", "SUBFAMILY"
# , "TRIBE", "GENUS"
# , "HABIT", "FFG", "LIFE_CYCLE", "THERMAL_INDICATOR"
# , "FFG2", "HABITAT"
# , "ELEVATION_ATTR", "GRADIENT_ATTR", "WSAREA_ATTR")
col2upper <- col.req_character[!(col.req_character %in%
c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS"))]
# #myDF <- apply(myDF[, col2upper], 2, toupper)
for (i in col2upper) {
myDF[, i] <- toupper(myDF[, i])
}## FOR ~ i ~ END
# use toupper() earlier, don't need
# removed as causing issues with shiny.io with some missing fields
# 2022-02-21, previous no longer present, redo here (all fields now present)
# Add extra columns for some fields
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "CN, CB" is both "CN" and "CB"
if (verbose == TRUE) {
debug_topic <- "Munging, TF"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Remove white space
myDF[, "HABIT"] <- gsub(" ","", myDF[, "HABIT"])
myDF[, "FFG"] <- gsub(" ","", myDF[, "FFG"])
myDF[, "LIFE_CYCLE"] <- gsub(" ","", myDF[, "LIFE_CYCLE"])
myDF[, "FFG2"] <- gsub(" ","", myDF[, "FFG2"])
myDF[, "THERMAL_INDICATOR"] <- gsub(" ","", myDF[, "THERMAL_INDICATOR"])
myDF[, "HABSTRUCT"] <- gsub(" ","", myDF[, "HABSTRUCT"])
myDF[, "ELEVATION_ATTR"] <- gsub(" ","", myDF[, "ELEVATION_ATTR"])
myDF[, "GRADIENT_ATTR"] <- gsub(" ","", myDF[, "GRADIENT_ATTR"])
myDF[, "WSAREA_ATTR"] <- gsub(" ","", myDF[, "WSAREA_ATTR"])
# code new columns
## match, any
myDF[, "HABIT_BU"] <- grepl("BU", myDF[, "HABIT"])
myDF[, "HABIT_CB"] <- grepl("CB", myDF[, "HABIT"])
myDF[, "HABIT_CN"] <- grepl("CN", myDF[, "HABIT"])
myDF[, "HABIT_SK"] <- grepl("SK", myDF[, "HABIT"])
myDF[, "HABIT_SP"] <- grepl("SP", myDF[, "HABIT"])
myDF[, "HABIT_SW"] <- grepl("SW", myDF[, "HABIT"])
myDF[, "FFG_COL"] <- grepl("(CG|GC)", myDF[, "FFG"])
myDF[, "FFG_FIL"] <- grepl("(CF|FC)", myDF[, "FFG"])
myDF[, "FFG_PRE"] <- grepl("PR", myDF[, "FFG"])
myDF[, "FFG_SCR"] <- grepl("SC", myDF[, "FFG"])
myDF[, "FFG_SHR"] <- grepl("SH", myDF[, "FFG"])
myDF[, "FFG_MAH"] <- grepl("MH", myDF[, "FFG"]) # macrophyte herbivore
myDF[, "FFG_OMN"] <- grepl("OM", myDF[, "FFG"])
myDF[, "FFG_PAR"] <- grepl("PA", myDF[, "FFG"])
myDF[, "FFG_PIH"] <- grepl("PH", myDF[, "FFG"])
myDF[, "FFG_XYL"] <- grepl("XY", myDF[, "FFG"])
myDF[, "LC_MULTI"] <- grepl("MULTI", myDF[, "LIFE_CYCLE"])
myDF[, "LC_SEMI"] <- grepl("SEMI", myDF[, "LIFE_CYCLE"])
myDF[, "LC_UNI"] <- grepl("UNI", myDF[, "LIFE_CYCLE"])
myDF[, "FFG2_PRE"] <- grepl("PR", myDF[, "FFG2"])
myDF[, "TI_STENOCOLD"] <- grepl("STENOC", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COLD"] <- grepl("COLD", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COOL"] <- grepl("COOL", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_WARM"] <- grepl("WARM", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_STENOWARM"] <- grepl("STENOW", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_EURY"] <- grepl("EURYTHERMAL", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COWA"] <- grepl("COWA", myDF[,"THERMAL_INDICATOR"])
myDF[, "HS_CS"] <- grepl("CS", myDF[, "HABSTRUCT"])
myDF[, "HS_NF"] <- grepl("NF", myDF[, "HABSTRUCT"])
myDF[, "HS_RM"] <- grepl("RM", myDF[, "HABSTRUCT"])
myDF[, "HS_SG"] <- grepl("SG", myDF[, "HABSTRUCT"])
## match, exact only
myDF[, "TI_NA"] <- is.na(myDF[, "THERMAL_INDICATOR"]) |
myDF[, "THERMAL_INDICATOR"] == ""
myDF[, "HABITAT_BRAC"] <- "BRAC" == myDF[, "HABITAT"]
myDF[, "HABITAT_DEPO"] <- "DEPO" == myDF[, "HABITAT"]
myDF[, "HABITAT_GENE"] <- "GENE" == myDF[, "HABITAT"]
myDF[, "HABITAT_HEAD"] <- "HEAD" == myDF[, "HABITAT"]
myDF[, "HABITAT_LENT"] <- "LENT" == myDF[, "HABITAT"]
myDF[, "HABITAT_LOTI"] <- "LOTI" == myDF[, "HABITAT"]
myDF[, "HABITAT_RHEO"] <- "RHEO" == myDF[, "HABITAT"]
myDF[, "HABITAT_RIVE"] <- "RIVE" == myDF[, "HABITAT"]
myDF[, "HABITAT_SPEC"] <- "SPEC" == myDF[, "HABITAT"]
myDF[, "HABITAT_TERR"] <- "TERR" == myDF[, "HABITAT"]
myDF[, "HABITAT_UNKN"] <- "UNKN" == myDF[, "HABITAT"]
myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"]
myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"]
myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"]
myDF[, "WSAREA_S"] <- "SMALL" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_M"] <- "MEDIUM" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_L"] <- "LARGE" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_XL"] <- "XLARGE" == myDF[, "WSAREA_ATTR"]
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# skip above in testing
# myDF[, "HABIT_BU"] <- FALSE
# myDF[, "HABIT_CB"] <- FALSE
# myDF[, "HABIT_CN"] <- FALSE
# myDF[, "HABIT_SP"] <- FALSE
# myDF[, "HABIT_SW"] <- FALSE
# myDF[, "FFG_COL"] <- FALSE
# myDF[, "FFG_FIL"] <- FALSE
# myDF[, "FFG_PRE"] <- FALSE
# myDF[, "FFG_SCR"] <- FALSE
# myDF[, "FFG_SHR"] <- FALSE
# myDF[, "LC_MULTI"] <- FALSE
# myDF[, "LC_SEMI"] <- FALSE
# myDF[, "LC_UNI"] <- FALSE
# # exact matches only
# myDF[, "TI_COLD"] <- FALSE
# myDF[, "TI_COLDCOOL"] <- FALSE
# myDF[, "TI_COOLWARM"] <- FALSE
# myDF[, "TI_WARM"] <- FALSE
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Calculate Metrics (could have used pipe, %>%)
# met.val <- myDF %>%
# dplyr::group_by(SAMPLEID, INDEX_NAME, INDEX_CLASS) %>%
# dplyr::summarise(ni_total=sum(N_TAXA)
# , nt_total=dplyr::n_distinct(TAXAID[EXCLUDE != TRUE], na.rm = TRUE)
# , ni_max= max(N_TAXA)
# , ni_dom01=dplyr::top_n(n=1, wt=N_TAXA)
# )
#https://stackoverflow.com/questions/45365484/how-to-find-top-n-descending-values-in-group-in-dplyr
# may have to create a 2nd output with domX metrics then join together.
# dom.val <- myDF %>%
# group_by(SAMPLEID, INDEX_NAME, INDEX_CLASS) %>%
# summarise(N_TAXA=n()) %>%
# top_n(n=3, wt=N_TAXA) %>%
# arrange()
# https://groups.google.com/forum/#!topic/manipulatr/ZzohinbNsJc
# X <- myDF %>% arrange(SampleID, desc(N_Taxa)) %>%
# group_by(SampleID) %>%
# filter(row_number()<=5)
# Create Dominant N ####
# Create df for Top N (without ties)
if (verbose == TRUE) {
debug_topic <- "Munging, Dom"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# DF for dom so same taxa get combined
# 2023-10-24, remove taxaid_dni
myDF_dom <- dplyr::summarise(dplyr::group_by(myDF
, INDEX_NAME
, INDEX_CLASS
, SAMPLEID
, TAXAID
, GENUS
, ORDER
, BCG_ATTR)
, N_TAXA = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last") %>%
dplyr::filter(!TAXAID %in% taxaid_dni) # doesn't work if do first
df.dom01 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom02 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom03 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 3)
df.dom04 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 4)
df.dom05 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 5)
df.dom06 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 6)
df.dom07 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 7)
df.dom08 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 8)
df.dom09 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 9)
df.dom10 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 10)
df.dom02_NoJugaRiss_BCG_att456 <- dplyr::arrange(myDF_dom, SAMPLEID
, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter((is.na(GENUS) == TRUE | GENUS != "JUGA")
& (is.na(ORDER) == TRUE | ORDER != "RISSOOIDEA")
& (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom01_BCG_att4 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(BCG_ATTR == "4") %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom01_BCG_att5 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(BCG_ATTR == "5") %>%
dplyr::filter(dplyr::row_number() <= 1)
# Summarise Top N
df.dom01.sum <- dplyr::summarise(dplyr::group_by(df.dom01
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02.sum <- dplyr::summarise(dplyr::group_by(df.dom02
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom03.sum <- dplyr::summarise(dplyr::group_by(df.dom03
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom03 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom04.sum <- dplyr::summarise(dplyr::group_by(df.dom04
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom04 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom05.sum <- dplyr::summarise(dplyr::group_by(df.dom05
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom05 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom06.sum <- dplyr::summarise(dplyr::group_by(df.dom06
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom06 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom07.sum <- dplyr::summarise(dplyr::group_by(df.dom07
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom07 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom08.sum <- dplyr::summarise(dplyr::group_by(df.dom08
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom08 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom09.sum <- dplyr::summarise(dplyr::group_by(df.dom09
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom09 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom10.sum <- dplyr::summarise(dplyr::group_by(df.dom10
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom10 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02_NoJugaRiss_BCG_att456.sum <- dplyr::summarise(dplyr::group_by(df.dom02_NoJugaRiss_BCG_att456
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02_NoJugaRiss_BCG_att456 = sum(N_TAXA)
, .groups = "drop_last")
df.dom01_BCG_att4.sum <- dplyr::summarise(dplyr::group_by(df.dom01_BCG_att4
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_BCG_att4 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom01_BCG_att5.sum <- dplyr::summarise(dplyr::group_by(df.dom01_BCG_att5
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_BCG_att5 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# Add column of domN to main DF
myDF <- merge(myDF, df.dom01.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom03.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom04.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom05.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom06.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom07.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom08.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom09.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom10.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02_NoJugaRiss_BCG_att456.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom01_BCG_att4.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom01_BCG_att5.sum, all.x = TRUE)
# Convert NA to 0 (avoid -Inf in later calculations)
myDF[is.na(myDF[, "ni_dom02_NoJugaRiss_BCG_att456"])
, "ni_dom02_NoJugaRiss_BCG_att456"] <- 0
myDF[is.na(myDF[, "ni_dom01_BCG_att4"]), "ni_dom01_BCG_att4"] <- 0
myDF[is.na(myDF[, "ni_dom01_BCG_att5"]), "ni_dom01_BCG_att5"] <- 0
# Clean up extra Dom data frames
rm(myDF_dom)
rm(df.dom01)
rm(df.dom02)
rm(df.dom03)
rm(df.dom04)
rm(df.dom05)
rm(df.dom06)
rm(df.dom07)
rm(df.dom08)
rm(df.dom09)
rm(df.dom10)
rm(df.dom02_NoJugaRiss_BCG_att456)
rm(df.dom01_BCG_att4)
rm(df.dom01_BCG_att5)
rm(df.dom01.sum)
rm(df.dom02.sum)
rm(df.dom03.sum)
rm(df.dom04.sum)
rm(df.dom05.sum)
rm(df.dom06.sum)
rm(df.dom07.sum)
rm(df.dom08.sum)
rm(df.dom09.sum)
rm(df.dom10.sum)
rm(df.dom02_NoJugaRiss_BCG_att456.sum)
rm(df.dom01_BCG_att4.sum)
rm(df.dom01_BCG_att5.sum)
# Metric Calc -----
if (verbose == TRUE) {
debug_topic <- "Calc, metrics"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
time_start2 <- Sys.time()
# Need for metrics without taxaid_dni
myDF.dni_F <- dplyr::filter(myDF, !TAXAID %in% taxaid_dni)
if (metric_subset == "MTTI") {
## Metric Calc, MTTI ----
### met.val, DNI = FALSE----
met.val.dni_F <- dplyr::summarise(dplyr::group_by(myDF.dni_F
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
#
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
# WAopt
, x_tv2_min = min(TOLVAL2, na.rm = TRUE)
, x_tv2_max = max(TOLVAL2, na.rm = TRUE)
, .groups = "drop_last"
)## met.val.dni_F ~ END
### met.val, DNI = TRUE----
met.val.dni_T <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
#### totals ----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
#### DNI ----
, nt_dni = sum(TAXAID == "DNI", na.rm = TRUE)
, pi_dni = 100 * sum(N_TAXA[TAXAID == "DNI"]
, na.rm = TRUE) / ni_total
, pt_dni = 100 * nt_dni / nt_total
, .groups = "drop_last"
)## met.val.dni_F ~ END
### met.val, join----
cols2match <- c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS")
met_dni <- c("nt_dni", "pi_dni", "pt_dni")
met.val <- dplyr::left_join(met.val.dni_F
, met.val.dni_T[, c(cols2match, met_dni)])
} else {
## Metric Calc, ALL ----
### met.val, DNI = FALSE----
met.val.dni_F <- dplyr::summarise(dplyr::group_by(myDF.dni_F
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
### Individuals ####
, ni_total = sum(N_TAXA, na.rm = TRUE)
, ni_totalNoDeca = sum(N_TAXA[is.na(ORDER) == TRUE |
ORDER != "DECAPODA"], na.rm = TRUE)
, li_total = log(ni_total)
, ni_Chiro = sum(N_TAXA[FAMILY == "CHIRONOMIDAE"], na.rm = TRUE)
, ni_Dipt = sum(N_TAXA[ORDER == "DIPTERA"], na.rm = TRUE)
, ni_EPT = sum(N_TAXA[ORDER == "EPHEMEROPTERA" |
ORDER == "PLECOPTERA" |
ORDER == "TRICHOPTERA"], na.rm = TRUE)
, ni_Trich = sum(N_TAXA[ORDER == "TRICHOPTERA"], na.rm = TRUE)
, ni_Americo = sum(N_TAXA[GENUS == "AMERICOROPHIUM"], na.rm = TRUE)
, ni_Gnorimo = sum(N_TAXA[GENUS == "GNORIMOSPHAEROMA"], na.rm = TRUE)
, ni_brackish = ni_Americo + ni_Gnorimo
, ni_Ramello = sum(N_TAXA[GENUS == "RAMELLOGAMMARUS"], na.rm = TRUE)
### Phylo ####
#### nt_phylo ----
# account for "NONE" in nt_total, should be the only 0 N_TAXA
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
, nt_Amph = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "AMPHIPODA"]
, na.rm = TRUE)
, nt_Bival = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "BIVALVIA"]
, na.rm = TRUE)
, nt_Capit = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CAPITELLIDAE"]
, na.rm = TRUE)
, nt_Caridea = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& INFRAORDER == "CARIDEA"]
, na.rm = TRUE)
#, nt_Chiro ## in special Chironomidae section
, nt_Coleo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, nt_COET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_COETNoBraBaeHydTri = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "BRACHYCENTRUS")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE)
, nt_CruMol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE)
, nt_Deca = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "DECAPODA"]
, na.rm = TRUE)
, nt_Dipt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "DIPTERA"]
, na.rm = TRUE)
, nt_ECT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "COLEOPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_Ephem = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, nt_EphemNoBaeTri = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE)
, nt_Ephemerellid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "EPHEMERELLIDAE"]
, na.rm = TRUE)
, nt_EPT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_ET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_Gast = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "GASTROPODA"]
, na.rm = TRUE)
, nt_Hemipt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "HEMIPTERA"]
, na.rm = TRUE)
, nt_Hepta = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "HEPTAGENIIDAE"]
, na.rm = TRUE)
, nt_Insect = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "INSECTA"]
, na.rm = TRUE)
, nt_Isop = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ISOPODA"]
, na.rm = TRUE)
, nt_Mega = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "MEGALOPTERA"]
, na.rm = TRUE)
, nt_Mol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"]
, na.rm = TRUE)
, nt_Nereid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "NEREIDIDAE"]
, na.rm = TRUE)
, nt_Nemour = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "NEMOURIDAE"]
, na.rm = TRUE)
, nt_NonIns = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (CLASS != "INSECTA"
| is.na(CLASS))]
, na.rm = TRUE)
, nt_Nudib = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "NUDIBRANCHIA"]
, na.rm = TRUE)
, nt_Odon = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ODONATA"]
, na.rm = TRUE)
, nt_OET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")]
, na.rm = TRUE)
, nt_Oligo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA")]
, na.rm = TRUE)
, nt_Perlid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "PERLIDAE"]
, na.rm = TRUE)
, nt_Pleco = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "PLECOPTERA"]
, na.rm = TRUE)
, nt_POET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")]
, na.rm = TRUE)
, nt_POETNoBae = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")]
, na.rm = TRUE)
, nfam_Baetidae = dplyr::n_distinct(FAMILY[EXCLUDE != TRUE
& FAMILY == "BAETIDAE"]
, na.rm = TRUE)
, nt_POETfamBae = nt_POETNoBae + nfam_Baetidae
, nt_Poly = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "POLYCHAETA"]
, na.rm = TRUE)
, nt_PolyNoSpion = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "POLYCHAETA"
& (is.na(FAMILY) == TRUE
| FAMILY != "SPIONIDAE")]
, na.rm = TRUE)
, nt_Ptero = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GENUS == "PTERONARCYS"]
, na.rm = TRUE)
, nt_Rhya = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GENUS == "RHYACOPHILA"]
, na.rm = TRUE)
, nt_Spion = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "SPIONIDAE"]
, na.rm = TRUE)
, nt_Tipulid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "TIPULIDAE"]
, na.rm = TRUE)
, nt_Trich = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
, nt_TrichNoHydro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE")]
, na.rm = TRUE)
, nt_Tromb = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TROMBIDIFORMES"]
, na.rm = TRUE)
, nt_Tubif = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "TUBIFICIDAE"]
, na.rm = TRUE)
# ,intolMol, ,
#### pi_phylo ####
, pi_Ampe = NA #pi_Ampeliscidae
, pi_AmpeHaust = NA
, pi_Amph = 100 * sum(N_TAXA[ORDER == "AMPHIPODA"]
, na.rm = TRUE) / ni_total
, pi_AmphIsop = 100 * sum(N_TAXA[ORDER == "AMPHIPODA"
| ORDER == "ISOPODA"]
, na.rm = TRUE) / ni_total
, pi_Baet = 100 * sum(N_TAXA[FAMILY == "BAETIDAE"]
, na.rm = TRUE) / ni_total
#, pi_Baet2Ephem
, pi_Bival = 100 * sum(N_TAXA[CLASS == "BIVALVIA"]
, na.rm = TRUE) / ni_total
, pi_Caen = 100 * sum(N_TAXA[FAMILY == "CAENIDAE"]
, na.rm = TRUE) / ni_total
, pi_Capit = 100 * sum(N_TAXA[FAMILY == "CAPITELLIDAE"]
, na.rm = TRUE) / ni_total
, pi_Cheu = 100 * sum(N_TAXA[GENUS == "CHEUMATOPSYCHE"]
, na.rm = TRUE) / ni_total
, pi_CheuSimHyalella = 100 * sum(N_TAXA[GENUS == "CHEUMATOPSYCHE"
| GENUS == "SIMULIUM"
| GENUS == "HYALELLA"]
, na.rm = TRUE) / ni_total
, pi_Cirra = 100 * sum(N_TAXA[FAMILY == "CIRRATULIDAE"]
, na.rm = TRUE) / ni_total
, pi_Clite = 100 * sum(N_TAXA[CLASS == "CLITELLATA"]
, na.rm = TRUE) / ni_total
, pi_Coleo = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"]
, na.rm = TRUE) / ni_total
, pi_COET = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Corb = 100 * sum(N_TAXA[GENUS == "CORBICULA"]
, na.rm = TRUE) / ni_total
, pi_CorixPhys = 100 * sum(N_TAXA[FAMILY == "CORIXIDAE"
| FAMILY == "PHYSIDAE"]
, na.rm = TRUE) / ni_total
, pi_CraCaeGam = 100 * sum(N_TAXA[GENUS == "CRANGONYX"
| GENUS == "CAECIDOTEA"
| GENUS == "GAMMARUS"]
, na.rm = TRUE) / ni_total
, pi_Cru = 100 * sum(N_TAXA[SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE) / ni_total
, pi_CruMol = 100 * sum(N_TAXA[PHYLUM == "MOLLUSCA"
| SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE) / ni_total
, pi_Deca = 100 * sum(N_TAXA[ORDER == "DECAPODA"]
, na.rm = TRUE) / ni_total
, pi_Dipt = 100 * sum(N_TAXA[ORDER == "DIPTERA"]
, na.rm = TRUE) / ni_total
, pi_DiptNonIns = 100 * sum(N_TAXA[ORDER == "DIPTERA"
| CLASS != "INSECTA"
| is.na(CLASS)]
, na.rm = TRUE) / ni_total
, pi_ECT = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "COLEOPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Ephem = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE) / ni_total
, pi_EphemNoCae = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "CAENIDAE")]
, na.rm = TRUE) / ni_total
, pi_EphemNoCaeBae = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "CAENIDAE")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")]
, na.rm = TRUE) / ni_total
, pi_EphemNoBaeTri = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE) / ni_total
, pi_EPT = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_EPTNoBaeHydro = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE"))
| (ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE"))
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_EPTNoCheu = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA"
& (is.na(GENUS) == TRUE
| GENUS != "CHEUMATOPSYCHE")]
, na.rm = TRUE) / ni_total
, pi_EPTNoHydro = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA")
| (ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE"))
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_ET = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Gast = 100 * sum(N_TAXA[CLASS == "GASTROPODA"]
, na.rm = TRUE) / ni_total
, pi_Haust = 100 * sum(N_TAXA[FAMILY == "HAUSTORIIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hemipt = 100 * sum(N_TAXA[ORDER == "HEMIPTERA"]
, na.rm = TRUE) / ni_total
, pi_Hesion = 100 * sum(N_TAXA[FAMILY == "HESIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hydro = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hydro2EPT = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE)/ni_EPT
, pi_Hydro2Trich = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE)/ni_Trich
, pi_Insect = 100 * sum(N_TAXA[CLASS == "INSECTA"]
, na.rm = TRUE) / ni_total
, pi_Isop = 100 * sum(N_TAXA[ORDER == "ISOPODA"]
, na.rm = TRUE) / ni_total
, pi_IsopGastHiru = 100 * sum(N_TAXA[ORDER == "ISOPODA"
| CLASS == "GASTROPODA"
| SUBCLASS == "HIRUDINEA"]
, na.rm = TRUE) / ni_total
, pi_Juga = 100 * sum(N_TAXA[GENUS == "JUGA"]
, na.rm = TRUE) / ni_total
, pi_JugaFlumi = 100 * sum(N_TAXA[GENUS == "JUGA"
| GENUS == "FLUMINICOLA"]
, na.rm = TRUE) / ni_total
, pi_Lucin = 100 * sum(N_TAXA[FAMILY == "LUCINIDAE"]
, na.rm = TRUE) / ni_total
, pi_LucinTellin = 100 * sum(N_TAXA[FAMILY == "LUCINIDAE"
| FAMILY == "TELLINIDAE"]
, na.rm = TRUE) / ni_total
, pi_Mega = 100 * sum(N_TAXA[ORDER == "MEGALOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Mol = 100 * sum(N_TAXA[PHYLUM == "MOLLUSCA"]
, na.rm = TRUE) / ni_total
, pi_Nemata = 100 * sum(N_TAXA[PHYLUM == "NEMATA"]
, na.rm = TRUE) / ni_total
, pi_Nereid = 100 * sum(N_TAXA[FAMILY == "NEREIDIDAE"]
, na.rm = TRUE) / ni_total
, pi_Nudib = 100 * sum(N_TAXA[ORDER == "NUDIBRANCHIA"]
, na.rm = TRUE) / ni_total
, pi_NonIns = 100 * sum(N_TAXA[CLASS != "INSECTA"
| is.na(CLASS)]
, na.rm = TRUE) / ni_total
, pi_Odon = 100 * sum(N_TAXA[ORDER == "ODONATA"]
, na.rm = TRUE) / ni_total
, pi_OET = 100 * sum(N_TAXA[ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Oligo = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"]
, na.rm = TRUE) / ni_total
, pi_OligoChiroHydro = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"
| FAMILY == "CHIRONOMIDAE"
| FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE) / ni_total
, pi_OligoHiru = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"
| SUBCLASS == "HIRUDINEA"]
, na.rm = TRUE) / ni_total
, pi_Orbin = 100 * sum(N_TAXA[FAMILY == "ORBINIIDAE"]
, na.rm = TRUE) / ni_total
, pi_Pleco = 100 * sum(N_TAXA[ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_POET = 100 * sum(N_TAXA[ORDER == "PLECOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Poly = 100 * sum(N_TAXA[CLASS == "POLYCHAETA"]
, na.rm = TRUE) / ni_total
, pi_Spion = 100 * sum(N_TAXA[FAMILY == "SPIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Spion2Poly = 100 * sum(N_TAXA[CLASS == "POLYCHAETA" |
FAMILY == "SPIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Sphaer = 100 * sum(N_TAXA[FAMILY == "SPHAERIIDAE"]
, na.rm = TRUE) / ni_total
, pi_SphaerCorb = 100 * sum(N_TAXA[FAMILY == "SPHAERIIDAE" |
GENUS == "CORBICULA"]
, na.rm = TRUE) / ni_total
, pi_Tellin = 100 * sum(N_TAXA[FAMILY == "TELLINIDAE"]
, na.rm = TRUE) / ni_total
, pi_Trich = 100 * sum(N_TAXA[ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_TrichNoHydro = 100 * sum(N_TAXA[ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE |
FAMILY != "HYDROPSYCHIDAE")]
, na.rm = TRUE) / ni_total
, pi_Tromb = 100 * sum(N_TAXA[ORDER == "TROMBIDIFORMES"]
, na.rm = TRUE) / ni_total
, pi_Tubif = 100 * sum(N_TAXA[FAMILY == "TUBIFICIDAE"]
, na.rm = TRUE) / ni_total
, pi_Xanth = 100 * sum(N_TAXA[FAMILY == "XANTHIDAE"]
, na.rm = TRUE) / ni_total
# Cole2Odon,
#EPTsenstive in tolerance group
#### pt_phylo ####
, pt_Amph = 100 * nt_Amph / nt_total
, pt_Bival = 100 * nt_Bival / nt_total
, pt_Coleo = 100 * nt_Coleo / nt_total
, pt_COET = 100 * nt_COET / nt_total
, pt_Deca = 100 * nt_Deca / nt_total
, pt_Dipt = 100 * nt_Dipt / nt_total
, pt_ECT = 100 * nt_ECT / nt_total
, pt_Ephem = 100 * nt_Ephem / nt_total
, pt_EPT = 100 * nt_EPT / nt_total
, pt_ET = 100 * nt_ET / nt_total
, pt_Gast = 100 * nt_Gast / nt_total
, pt_Hemipt = 100 * nt_Hemipt / nt_total
, pt_Insect = 100 * nt_Insect / nt_total
, pt_Isop = 100 * nt_Isop / nt_total
, pt_Mega = 100 * nt_Mega / nt_total
, pt_NonIns = 100 * nt_NonIns / nt_total
, pt_Nudib = 100 * nt_Nudib / nt_total
, pt_Odon = 100 * nt_Odon / nt_total
, pt_OET = 100 * nt_OET / nt_total
, pt_Oligo = 100 * nt_Oligo / nt_total
, pt_Pleco = 100 * nt_Pleco / nt_total
, pt_POET = 100 * nt_POET / nt_total
, pt_Poly = 100 * nt_Poly / nt_total
, pt_PolyNoSpion = 100 * nt_PolyNoSpion / nt_total
, pt_Spion = 100 * nt_Spion / nt_total
, pt_Trich = 100 * nt_Trich / nt_total
, pt_TrichNoHydro = 100 * nt_TrichNoHydro / nt_total
, pt_Tromb = 100 * nt_Tromb / nt_total
#### ratio_phylo ####
# nt_X / log(ni_total)
# X = specialty group, e.g., Bivalves
# Log is natural log
#, rt_Amph = nt_Amph
#, rt_AmpCar = nt_AmpCar
#, rt_Bivalve = nt_Bivalve
#, rt_Capit = nt_Capit
#, rt_Car = nt_Car
#, rt_Coleo = nt_Coleo
#, rt_CruMol = nt_CruMol
#, rt_Deca = nt_Deca
#, rt_Ephem = nt_Ephem
#, rt_EPT = nt_EPT
#, rt_Gast = nt_Gast
#, rt_Isop = nt_Isop
#, rt_Nereid = nt_Nereid
#, rt_Nudib = nt_Nudib
#, rt_Oligo = nt_Oligo
#, rt_Pleco = nt_Pleco
#, rt_Poly = nt_Poly
#, rt_PolyNoSpion = nt_PolyNoSpion
#, rt_Ptero = nt_Ptero
#, rt_Spion = nt_Spion
#, rt_Trich = nt_Trich
#, rt_Tubif = nt_Tubif
### Midges ####
# Family = Chironomidae
# subfamily = Chironominae
# subfamily = Orthocladiinae
# subfamily = Tanypodinae
# Tribe = Tanytarsini
, nt_Chiro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CHIRONOMIDAE"]
, na.rm = TRUE)
, pi_Chiro = 100 * ni_Chiro / ni_total
, pt_Chiro = 100 * nt_Chiro / nt_total
, pi_Ortho = 100 * sum(N_TAXA[SUBFAMILY == "ORTHOCLADIINAE"]
, na.rm = TRUE) / ni_total
, pi_Tanyt = 100 * sum(N_TAXA[TRIBE == "TANYTARSINI"]
, na.rm = TRUE) / ni_total
, pi_Tanyp = 100 * sum(N_TAXA[SUBFAMILY == "TANYPODINAE"]
, na.rm = TRUE) / ni_total
, pi_Chi2Dipt = 100 * ni_Chiro / ni_Dipt
, pi_COC2Chi = 100 * sum(N_TAXA[GENUS == "CHIRONOMUS"
| GENUS == "CRICOTOPUS"
| GENUS == "CRICOTOPUS/ORTHOCLADIUS"
| GENUS == "ORTHOCLADIUS/CRICOTOPUS"
| GENUS == "ORTHOCLADIUS"]
, na.rm = TRUE)/ni_Chiro
, pi_ChCr2Chi = 100 * sum(N_TAXA[GENUS == "CHIRONOMUS"
| GENUS == "CRICOTOPUS"]
, na.rm = TRUE)/ni_Chiro
, pi_Orth2Chi = 100 * sum(N_TAXA[SUBFAMILY == "ORTHOCLADIINAE"]
, na.rm = TRUE)/ni_Chiro
, pi_Tanyp2Chi = 100 * sum(N_TAXA[SUBFAMILY == "TANYPODINAE"]
, na.rm = TRUE)/ni_Chiro
#,nt_Ortho (Marine)
#MB_pi_OrthocladiinaeCricotopusChironomus2Chironomidae
# rt_Chiro, Ortho, Tanyt
, pi_ChiroAnne = 100 * sum(N_TAXA[PHYLUM == "ANNELIDA"
| FAMILY == "CHIRONOMIDAE"]
, na.rm = TRUE) / ni_total
### Other misc ----
# dominant
, pi_dom02_BCG_att456_NoJugaRiss = 100 * max(ni_dom02_NoJugaRiss_BCG_att456) / ni_total
#
# 20180608, rework PacNW
# NonINSECTA, Attribute 456
, nt_NonIns_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonIns_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonIns_BCG_att456 = 100 * nt_NonIns_BCG_att456 / nt_total
# NonInsectaJugaRiss, Attribute 456
, nt_NonInsJugaRiss_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "RISSOOIDEA")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsJugaRiss_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "RISSOOIDEA")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsJugaRiss_BCG_att456 = 100 * nt_NonInsJugaRiss_BCG_att456 / nt_total
# 20180815, Percent BAETIS TRICAUDATUS COMPLEX + SIMULIIDAE individual
, pi_SimBtri = 100 * (sum(N_TAXA[FAMILY == "SIMULIIDAE"], na.rm = TRUE)
+ sum(N_TAXA[TAXAID == "BAETIS TRICAUDATUS COMPLEX"]
, na.rm = TRUE)) / ni_total
# 20181018, MS, sensitive COLEOPTERA & (Family is Null or not Hydrophyilidae)
, pi_Colesens = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"
& (FAMILY != "HYDROPHILIDAE"
| is.na(FAMILY) == TRUE)]
, na.rm = TRUE) / ni_total
# 20181207, BCG PacNW, Level 1 Signal metrics
, nt_longlived = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LONGLIVED == TRUE]
, na.rm = TRUE)
, pt_longlived = 100 * nt_longlived / nt_total
, nt_noteworthy = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NOTEWORTHY == TRUE]
, na.rm = TRUE)
, nt_ffg2_pred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG2_PRE == TRUE]
, na.rm = TRUE)
, ni_Noto = sum(N_TAXA[GENUS == "NOTOMASTUS"], na.rm = TRUE)
### Thermal Indicators ----
#### nt_ti----
, nt_ti_stenocold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_STENOCOLD == TRUE]
, na.rm = TRUE)
, nt_ti_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COLD == TRUE]
, na.rm = TRUE)
, nt_ti_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COOL == TRUE]
, na.rm = TRUE)
, nt_ti_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_WARM == TRUE]
, na.rm = TRUE)
, nt_ti_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_STENOWARM == TRUE]
, na.rm = TRUE)
, nt_ti_eury = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_EURY == TRUE]
, na.rm = TRUE)
, nt_ti_cowa = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COWA == TRUE]
, na.rm = TRUE)
, nt_ti_na = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_NA == TRUE]
, na.rm = TRUE)
, nt_ti_stenocold_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_STENOCOLD == TRUE |
TI_COLD == TRUE)]
, na.rm = TRUE)
, nt_ti_stenocold_cold_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_STENOCOLD == TRUE |
TI_COLD == TRUE |
TI_COOL == TRUE)]
, na.rm = TRUE)
, nt_ti_cowa_warm_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_COWA == TRUE |
TI_WARM == TRUE |
TI_STENOWARM == TRUE )]
, na.rm = TRUE)
, nt_ti_warm_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_WARM == TRUE |
TI_STENOWARM == TRUE)]
, na.rm = TRUE)
#### pi_ti----
, pi_ti_stenocold = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cold = 100 * sum(N_TAXA[TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool = 100 * sum(N_TAXA[TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm = 100 * sum(N_TAXA[TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenowarm = 100 * sum(N_TAXA[TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_eury = 100 * sum(N_TAXA[TI_EURY == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cowa = 100 * sum(N_TAXA[TI_COWA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_na = 100 * sum(N_TAXA[TI_NA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenocold_cold = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE |
TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenocold_cold_cool = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE |
TI_COLD == TRUE |
TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cowa_warm_stenowarm = 100 * sum(N_TAXA[TI_COWA == TRUE |
TI_WARM == TRUE |
TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm_stenowarm = 100 * sum(N_TAXA[TI_WARM == TRUE |
TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
#### pt_ti ----
, pt_ti_stenocold = 100 * nt_ti_stenocold / nt_total
, pt_ti_cold = 100 * nt_ti_cold / nt_total
, pt_ti_cool = 100 * nt_ti_cool / nt_total
, pt_ti_warm = 100 * nt_ti_warm / nt_total
, pt_ti_stenowarm = 100 * nt_ti_stenowarm / nt_total
, pt_ti_eury = 100 * nt_ti_eury / nt_total
, pt_ti_cowa = 100 * nt_ti_cowa / nt_total
, pt_ti_na = 100 * nt_ti_na / nt_total
, pt_ti_stenocold_cold = 100 * nt_ti_stenocold_cold / nt_total
, pt_ti_stenocold_cold_cool = 100 * nt_ti_stenocold_cold_cool / nt_total
, pt_ti_cowa_warm_stenowarm = 100 * nt_ti_cowa_warm_stenowarm / nt_total
, pt_ti_warm_stenowarm = 100 * nt_ti_warm_stenowarm / nt_total
### ratio
, ri_ti_sccc_wsw = pi_ti_stenocold_cold_cool / pi_ti_warm_stenowarm
### Tolerance ----
# 4 and 6 are WV GLIMPSS (no equal)
, nt_tv_intol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 3]
, na.rm = TRUE)
, nt_tv_intol2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 2]
, na.rm = TRUE)
, nt_tv_intol4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL < 4]
, na.rm = TRUE)
, nt_tv_toler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 7
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_tv_toler6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 6
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_tv_toler8 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE)
, pi_tv_intol = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL <= 3], na.rm = TRUE) / ni_total
, pi_tv_intol4 = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL < 4], na.rm = TRUE) / ni_total
, pi_tv_toler = 100 * sum(N_TAXA[TOLVAL >= 7
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pi_tv_toler6 = 100 * sum(N_TAXA[TOLVAL > 6
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pi_tv_toler8 = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pt_tv_intol = 100 * nt_tv_intol / nt_total
, pt_tv_intol4 = 100 * nt_tv_intol4 / nt_total
, pt_tv_toler = 100 * nt_tv_toler / nt_total
, pt_tv_toler6 = 100 * nt_tv_toler6 / nt_total
, pt_tv_toler8 = 100 * nt_tv_toler8 / nt_total
#,nt_tvfam_intol = dplyr::n_distinct(TAXAID[EXCLUDE!=TRUE & FAM_TV<=3 & !is.na(FAM_TV)])
# pi_Baet2Eph, pi_Hyd2EPT, pi_Hyd2Tri, in Pct Ind group
# nt_intMol (for marine)
# intol4_EPT is PA not WV so [0-4].
, nt_tv_intol4_EPT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 4
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")]
, na.rm = TRUE)
# USEPA, WSA and NRSA
## ntol is not tolerant
## stol is super tolerant
, nt_tv_ntol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL < 6]
, na.rm = TRUE)
, nt_tv_stol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE)
, pi_tv_ntol = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL < 6]
, na.rm = TRUE) / ni_total
, pi_tv_stol = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE) / ni_total
, pt_tv_ntol = 100 * nt_tv_ntol / nt_total
, pt_tv_stol = 100 * nt_tv_stol / nt_total
### Tolerance2 ####
## special condition tolerance values
# MBSS
, pi_tv2_intol = sum(N_TAXA[TOLVAL2 <= 3
& !is.na(TOLVAL2)])/sum(N_TAXA[!is.na(TOLVAL2)])
#, pi_tv_intolurb=pi_tv2_intol
, pi_tv2_toler_ISA_SalHi_xFL = NA
, pi_tv2_intol_ISA_SalHi_xFL = NA
, pt_tv2_intol_ISA_SalHi_xFL = NA
### FFG #####
#### nt_ffg----
, nt_ffg_col = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_COL == TRUE]
, na.rm = TRUE)
, nt_ffg_filt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_FIL == TRUE]
, na.rm = TRUE)
, nt_ffg_pred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PRE == TRUE]
, na.rm = TRUE)
, nt_ffg_scrap = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_SCR == TRUE]
, na.rm = TRUE)
, nt_ffg_shred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_SHR == TRUE]
, na.rm = TRUE)
, nt_ffg_mah = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_MAH == TRUE]
, na.rm = TRUE)
, nt_ffg_omn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_OMN == TRUE]
, na.rm = TRUE)
, nt_ffg_par = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PAR == TRUE]
, na.rm = TRUE)
, nt_ffg_pih = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PIH == TRUE]
, na.rm = TRUE)
, nt_ffg_xyl = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_XYL == TRUE]
, na.rm = TRUE)
, nt_ffg_pred_scrap_shred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (FFG_PRE == TRUE |
FFG_SCR == TRUE |
FFG_SHR == TRUE)]
, na.rm = TRUE)
, nt_ffg_pred_NoChi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PRE == TRUE
& (is.na(FAMILY) == TRUE
| FAMILY != "CHIRONOMIDAE")]
, na.rm = TRUE)
#### pi_ffg----
, pi_ffg_col = 100 * sum(N_TAXA[FFG_COL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_filt = 100 * sum(N_TAXA[FFG_FIL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_pred = 100 * sum(N_TAXA[FFG_PRE == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_scrap = 100 * sum(N_TAXA[FFG_SCR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_shred = 100 * sum(N_TAXA[FFG_SHR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_mah = 100 * sum(N_TAXA[FFG_MAH == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_omn = 100 * sum(N_TAXA[FFG_OMN == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_par = 100 * sum(N_TAXA[FFG_PAR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_pih = 100 * sum(N_TAXA[FFG_PIH == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_xyl = 100 * sum(N_TAXA[FFG_XYL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_col_filt = 100 * sum(N_TAXA[FFG_COL == TRUE |
FFG_FIL == TRUE]
, na.rm = TRUE) / ni_total
#### pt_ffg----
, pt_ffg_col = 100 * nt_ffg_col / nt_total
, pt_ffg_filt = 100 * nt_ffg_filt / nt_total
, pt_ffg_pred = 100 * nt_ffg_pred / nt_total
, pt_ffg_scrap = 100 * nt_ffg_scrap / nt_total
, pt_ffg_shred = 100 * nt_ffg_shred / nt_total
, pt_ffg_mah = 100 * nt_ffg_mah / nt_total
, pt_ffg_omn = 100 * nt_ffg_omn / nt_total
, pt_ffg_par = 100 * nt_ffg_par / nt_total
, pt_ffg_pih = 100 * nt_ffg_pih / nt_total
, pt_ffg_xyl = 100 * nt_ffg_xyl / nt_total
#, pi_ffg_infc
#, rt_ffg_infc, converborbelt, scavbrow, subsurf, watercol
#, rt_ffg_pred
# carnivoreomnivore, deepdeposit, suspension
### FFG2 ####
# marine
## nt_ffg2
, nt_ffg2_intface = NA
, nt_ffg2_subsurf = NA
## pi_ffg2
, pi_ffg2_scavburr = NA
## pt_ffg2
# = conveyorbelt, interface, scavengerbrowser, subsurface, watercolumn, predator
### Habit ####
#(need to be wild card. that is, counts both CN,CB and CB as climber)
#### nt_habit----
, nt_habit_burrow = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_BU == TRUE]
, na.rm = TRUE)
, nt_habit_climb = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_CB == TRUE]
, na.rm = TRUE)
, nt_habit_climbcling = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (HABIT_CB == TRUE
| HABIT_CN == TRUE)])
, nt_habit_cling = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_CN == TRUE]
, na.rm = TRUE)
, nt_habit_skate = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SK == TRUE]
, na.rm = TRUE)
, nt_habit_sprawl = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SP == TRUE]
, na.rm = TRUE)
, nt_habit_swim = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SW == TRUE]
, na.rm = TRUE)
#### pi_habit----
, pi_habit_burrow = 100 * sum(N_TAXA[HABIT_BU == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_climb = 100 * sum(N_TAXA[HABIT_CB == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_climbcling = 100 * sum(N_TAXA[HABIT_CB == TRUE
| HABIT_CN == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_cling = 100 * sum(N_TAXA[HABIT_CN == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_skate = 100 * sum(N_TAXA[HABIT_SK == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_sprawl = 100 * sum(N_TAXA[HABIT_SP == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_swim = 100 * sum(N_TAXA[HABIT_SW == TRUE]
, na.rm = TRUE) / ni_total
#### pt_habit----
, pt_habit_burrow = 100 * nt_habit_burrow / nt_total
, pt_habit_climb = 100 * nt_habit_climb / nt_total
, pt_habit_climbcling = 100 * nt_habit_climbcling / nt_total
, pt_habit_cling = 100 * nt_habit_cling / nt_total
, pt_habit_skate = 100 * nt_habit_sprawl / nt_total
, pt_habit_sprawl = 100 * nt_habit_sprawl / nt_total
, pt_habit_swim = 100 * nt_habit_swim / nt_total
## Oddball
# might not need habit != cling for Pleco
, pi_habit_cling_PlecoNoCling = 100 * sum(N_TAXA[HABIT_CN == TRUE
| (ORDER == "PLECOPTERA"
& HABIT_CN == FALSE)]
, na.rm = TRUE) / ni_total
### Life Cycle ####
# pi and nt for mltvol, semvol, univol
#### nt_LifeCycle----
, nt_volt_multi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_MULTI == TRUE]
, na.rm = TRUE)
, nt_volt_semi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_SEMI == TRUE]
, na.rm = TRUE)
, nt_volt_uni = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_UNI == TRUE]
, na.rm = TRUE)
#### pi_LifeCycle----
, pi_volt_multi = 100 * sum(N_TAXA[LC_MULTI == TRUE]
, na.rm = TRUE) / ni_total
, pi_volt_semi = 100 * sum(N_TAXA[LC_SEMI == TRUE]
, na.rm = TRUE) / ni_total
, pi_volt_uni = 100 * sum(N_TAXA[LC_UNI == TRUE]
, na.rm = TRUE) / ni_total
#### pt_LifeCycle----
, pt_volt_multi = 100 * nt_volt_multi / nt_total
, pt_volt_semi = 100 * nt_volt_semi / nt_total
, pt_volt_uni = 100 * nt_volt_uni / nt_total
### Dominant N ####
## uses previously defined values added to myDF
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
, pi_dom03 = 100 * max(ni_dom03, na.rm = TRUE) / ni_total
, pi_dom04 = 100 * max(ni_dom04, na.rm = TRUE) / ni_total
, pi_dom05 = 100 * max(ni_dom05, na.rm = TRUE) / ni_total
, pi_dom06 = 100 * max(ni_dom06, na.rm = TRUE) / ni_total
, pi_dom07 = 100 * max(ni_dom07, na.rm = TRUE) / ni_total
, pi_dom08 = 100 * max(ni_dom08, na.rm = TRUE) / ni_total
, pi_dom09 = 100 * max(ni_dom09, na.rm = TRUE) / ni_total
, pi_dom10 = 100 * max(ni_dom10, na.rm = TRUE) / ni_total
# , pi_dom01alt= dplyr::top_n(N_TAXA, n=1) / ni_total
#https://stackoverflow.com/questions/27766054/getting-the-top-values-by-group
# top_n uses ties so can't use it
### Indices ####
#, x_AMBI - may need extra function or like "top" functions do some precalc
#,x_Becks.CLASS1=n_distinct(N_TAXA[EXCLUDE!=TRUE & TolVal>=0 & TolVal<=2.5])
#,x_Becks.CLASS2=n_distinct(N_TAXA[EXCLUDE!=TRUE & TolVal>=2.5 & TolVal<=4])
, x_Becks = (2 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 1.5]
, na.rm = TRUE)) +
(1 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 1.5
& TOLVAL <= 4]
, na.rm = TRUE))
, x_Becks3 = (3 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 0.5]
, na.rm = TRUE)) +
(2 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 0.5
& TOLVAL <= 1.5]
, na.rm = TRUE)) +
(1 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 1.5
& TOLVAL <= 2.5]
, na.rm = TRUE))
#,x_HBI_numer=sum(N_TAXA*TOLVAL, na.rm = TRUE)
#,x_HBI_denom=sum(N_TAXA[!is.na(TOLVAL) & TOLVAL>=0], na.rm = TRUE)
, x_HBI = sum(N_TAXA * TOLVAL, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL)
& TOLVAL >= 0]
, na.rm = TRUE)
, x_HBI2 = sum(N_TAXA * TOLVAL2, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL2)
& TOLVAL2 >= 0]
, na.rm = TRUE)
, x_NCBI = sum(N_TAXA * TOLVAL2, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL2)
& TOLVAL2 >= 0]
, na.rm = TRUE)
, x_BCICTQa = sum(TOLVAL2[EXCLUDE != TRUE], na.rm = TRUE) / nt_total
# Shannon-Weiner
#, x_Shan_Num= -sum(log(N_TAXA / ni_total)), na.rm = TRUE)
#, x_Shan_e=x_Shan_Num/log(exp(1))
, x_Shan_e = -sum((N_TAXA / ni_total) * log((N_TAXA / ni_total))
, na.rm = TRUE)
, x_Shan_2 = x_Shan_e/log(2)
, x_Shan_10 = x_Shan_e/log(10)
#, x_D Simpson
, x_D = 1 - sum((N_TAXA / ni_total)^2, na.rm = TRUE)
#, X_D_G (Gleason) - [nt_total]/Log([ni_total])
, x_D_G = (nt_total) / log(ni_total)
#, x_D_Mg Margalef - ([nt_total]-1)/Log([ni_total])
, x_D_Mg = (nt_total - 1) / log(ni_total)
#, x_Hbe
#, x_H (Shannon)
# Evenness, Pielou
# H / Hmax Hmax is log(nt_total)
, x_Evenness = x_Shan_e/log(nt_total)
# evenness - different from Pielou in MS Coastal Metric Calc 2011 db
### Density ####
# Numbers per area sampled
### Estuary-Marine ####
# Mixed in with other metrics
, x_Becks_tv2 = NA
### Habitat ####
# BCG PacNW group 2020
# BRAC brackish
# DEPO depositional
# GENE generalist
# HEAD headwater
# RHEO rheophily
# RIVE riverine
# SPEC specialist
# UNKN unknown
#
#### nt_habitat----
, nt_habitat_brac = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_BRAC == TRUE]
, na.rm = TRUE)
, nt_habitat_depo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_DEPO == TRUE]
, na.rm = TRUE)
, nt_habitat_gene = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_GENE == TRUE]
, na.rm = TRUE)
, nt_habitat_head = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_HEAD == TRUE]
, na.rm = TRUE)
, nt_habitat_lent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_LENT == TRUE]
, na.rm = TRUE)
, nt_habitat_loti = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_LOTI == TRUE]
, na.rm = TRUE)
, nt_habitat_rheo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_RHEO == TRUE]
, na.rm = TRUE)
, nt_habitat_rive = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_RIVE == TRUE]
, na.rm = TRUE)
, nt_habitat_spec = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_SPEC == TRUE]
, na.rm = TRUE)
, nt_habitat_terr = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_TERR == TRUE]
, na.rm = TRUE)
, nt_habitat_unkn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_UNKN == TRUE]
, na.rm = TRUE)
#### pi_habitat----
, pi_habitat_brac = 100 * sum(N_TAXA[HABITAT_BRAC == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_depo = 100 * sum(N_TAXA[HABITAT_DEPO == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_gene = 100 * sum(N_TAXA[HABITAT_GENE == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_head = 100 * sum(N_TAXA[HABITAT_HEAD == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_lent = 100 * sum(N_TAXA[HABITAT_LENT == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_loti = 100 * sum(N_TAXA[HABITAT_LOTI == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_rheo = 100 * sum(N_TAXA[HABITAT_RHEO == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_rive = 100 * sum(N_TAXA[HABITAT_RIVE == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_spec = 100 * sum(N_TAXA[HABITAT_SPEC == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_terr = 100 * sum(N_TAXA[HABITAT_TERR == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_unkn = 100 * sum(N_TAXA[HABITAT_UNKN == TRUE]
, na.rm = TRUE) / ni_total
#### pt_habitat----
, pt_habitat_brac = 100 * nt_habitat_brac / nt_total
, pt_habitat_depo = 100 * nt_habitat_depo / nt_total
, pt_habitat_gene = 100 * nt_habitat_gene / nt_total
, pt_habitat_head = 100 * nt_habitat_head / nt_total
, pt_habitat_lent = 100 * nt_habitat_lent / nt_total
, pt_habitat_loti = 100 * nt_habitat_loti / nt_total
, pt_habitat_rheo = 100 * nt_habitat_rheo / nt_total
, pt_habitat_rive = 100 * nt_habitat_rive / nt_total
, pt_habitat_spec = 100 * nt_habitat_spec / nt_total
, pt_habitat_terr = 100 * nt_habitat_terr / nt_total
, pt_habitat_unkn = 100 * nt_habitat_unkn / nt_total
### BCG ####
# 1i, 1m, 1t
# Xi, Xm, Xt
# 5i, 5m, 5t
# 6i, 6m, 6t
# toupper(), 2022-02-22
#### BCG_nt----
, nt_BCG_att1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1"]
, na.rm = TRUE)
, nt_BCG_att1i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1I"]
, na.rm = TRUE)
, nt_BCG_att1m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1M"]
, na.rm = TRUE)
, nt_BCG_att12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
&
(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1i23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1i236i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att45 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att56 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att56t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_att6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att6i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att6m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6M")]
, na.rm = TRUE)
, nt_BCG_att6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_attNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(BCG_ATTR)]
, na.rm = TRUE)
, nt_BCG_att4b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_BCG_att4w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE)
, nt_BCG_att1i234b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_BETTER"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att4w5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
#### BCG_nt_Phylo----
, nt_Ephem_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_EPT_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_EPT_BCG_att1i23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_Pleco_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "PLECOPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_Trich_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_Coleo_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "COLEOPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Ephem_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Odon_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ODONATA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Trich_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
#### BCG_pi----
, pi_BCG_att1 = 100 * sum(N_TAXA[(BCG_ATTR == "1")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i = 100 * sum(N_TAXA[(BCG_ATTR == "1I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1m = 100 * sum(N_TAXA[(BCG_ATTR == "1M")]
, na.rm = TRUE) / ni_total
, pi_BCG_att12 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i2 = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att123 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i23 = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i236i = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att2 = 100 * sum(N_TAXA[(BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att23 = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att234 = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG_att3 = 100 * sum(N_TAXA[(BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4 = 100 * sum(N_TAXA[(BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG_att45 = 100 * sum(N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att456 = 100 * sum(N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5 = 100 * sum(N_TAXA[(BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5extra = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "5.5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56 = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56t = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6 = 100 * sum(N_TAXA[(BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6i = 100 * sum(N_TAXA[(BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6m = 100 * sum(N_TAXA[(BCG_ATTR == "6M")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6t = 100 * sum(N_TAXA[(BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_attNA = 100 * sum(N_TAXA[(is.na(BCG_ATTR) == TRUE)]
, na.rm = TRUE) / ni_total
, pi_BCG_att4b = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4m = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i234b = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_BETTER"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"]
, na.rm = TRUE)) / ni_total
, pi_BCG_att4w5 = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE)) / ni_total
#### BCG_pi_Phylo----
, pi_EPT_BCG_att123 = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_EPT_BCG_att1i23 = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
#### BCG_pt----
, pt_BCG_att1 = 100 * nt_BCG_att1 / nt_total
, pt_BCG_att1i = 100 * nt_BCG_att1i / nt_total
, pt_BCG_att1m = 100 * nt_BCG_att1m / nt_total
, pt_BCG_att12 = 100 * nt_BCG_att12 / nt_total
, pt_BCG_att1234 = 100 * nt_BCG_att1234 / nt_total
, pt_BCG_att1i2 = 100 * nt_BCG_att1i2 / nt_total
, pt_BCG_att123 = 100 * nt_BCG_att123 / nt_total
, pt_BCG_att1i23 = 100 * nt_BCG_att1i23 / nt_total
, pt_BCG_att1i236i = 100 * nt_BCG_att1i236i / nt_total
, pt_BCG_att2 = 100 * nt_BCG_att2 / nt_total
, pt_BCG_att23 = 100 * nt_BCG_att23 / nt_total
, pt_BCG_att234 = 100 * nt_BCG_att234 / nt_total
, pt_BCG_att3 = 100 * nt_BCG_att3 / nt_total
, pt_BCG_att4 = 100 * nt_BCG_att4 / nt_total
, pt_BCG_att45 = 100 * nt_BCG_att45 / nt_total
, pt_BCG_att456 = 100 * nt_BCG_att456 / nt_total
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
, pt_BCG_att56 = 100 * nt_BCG_att56 / nt_total
, pt_BCG_att56t = 100 * nt_BCG_att56t / nt_total
, pt_BCG_att6 = 100 * nt_BCG_att6 / nt_total
, pt_BCG_att6i = 100 * nt_BCG_att6i / nt_total
, pt_BCG_att6m = 100 * nt_BCG_att6m / nt_total
, pt_BCG_att6t = 100 * nt_BCG_att6t / nt_total
, pt_BCG_attNA = 100 * nt_BCG_attNA / nt_total
, pt_BCG_att4b = 100 * nt_BCG_att4b / nt_total
, pt_BCG_att4m = 100 * nt_BCG_att4m / nt_total
, pt_BCG_att4w = 100 * nt_BCG_att4w / nt_total
, pt_BCG_att1i234b = 100 * nt_BCG_att1i234b / nt_total
, pt_BCG_att4w5 = 100 * nt_BCG_att4w5 / nt_total
#### BCG_special ----
# BCG_pt_Phylo
, pt_EPT_BCG_att123 = 100 * nt_EPT_BCG_att123 / nt_total
, pt_EPT_BCG_att1i23 = 100 * nt_EPT_BCG_att1i23 / nt_total
#### BCG_pi_dom ----
, pi_dom01_BCG_att4 = 100 * max(0
, ni_dom01_BCG_att4
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5 = 100 * max(0
, ni_dom01_BCG_att5
, na.rm = TRUE) / ni_total
# domX_BCG
# pi_dom01_att 4, 5, 56
# pi_dom05_att 123, not 456
### UFC ----
#Taxonomic Uncertainty Frequency Class (use HBI calculation)
, x_UFC = sum(N_TAXA * UFC, na.rm = TRUE) / sum(N_TAXA[!is.na(UFC)
& UFC >= 1
& UFC <= 6]
, na.rm = TRUE)
### Elevation ----
, nt_elev_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ELEVATION_LOW == TRUE]
, na.rm = TRUE)
, nt_elev_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ELEVATION_HIGH == TRUE]
, na.rm = TRUE)
### Gradient ----
, nt_grad_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_LOW == TRUE]
, na.rm = TRUE)
, nt_grad_mod = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_MOD == TRUE]
, na.rm = TRUE)
, nt_grad_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_HIGH == TRUE]
, na.rm = TRUE)
### WS_Area ----
, nt_wsarea_small = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_S == TRUE]
, na.rm = TRUE)
, nt_wsarea_medium = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_M == TRUE]
, na.rm = TRUE)
, nt_wsarea_large = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_L == TRUE]
, na.rm = TRUE)
, nt_wsarea_xlarge = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_XL == TRUE]
, na.rm = TRUE)
### Habitat Structure ----
#### nt_habstruct----
, nt_habstruct_coarsesub = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_CS == TRUE]
, na.rm = TRUE)
, nt_habstruct_noflow = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_NF == TRUE]
, na.rm = TRUE)
, nt_habstruct_rootmat = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_RM == TRUE]
, na.rm = TRUE)
, nt_habstruct_snag = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_SG == TRUE]
, na.rm = TRUE)
, nt_habstruct_NA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(HABSTRUCT)]
, na.rm = TRUE)
#### pi_habstruct----
, pi_habstruct_coarsesub = 100 * sum(N_TAXA[HS_CS == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_noflow = 100 * sum(N_TAXA[HS_NF == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_rootmat = 100 * sum(N_TAXA[HS_RM == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_snag = 100 * sum(N_TAXA[HS_SG == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_NA = 100 * sum(N_TAXA[(is.na(HABSTRUCT) == TRUE)]
, na.rm = TRUE) / ni_total
#### pt_habstruct----
, pt_habstruct_coarsesub = 100 * nt_habstruct_coarsesub / nt_total
, pt_habstruct_noflow = 100 * nt_habstruct_noflow / nt_total
, pt_habstruct_rootmat = 100 * nt_habstruct_rootmat / nt_total
, pt_habstruct_snag = 100 * nt_habstruct_snag / nt_total
, pt_habstruct_NA = 100 * nt_habstruct_NA / nt_total
### nval_habstruct
, nval_habstruct = sum(HS_CS + HS_NF + HS_RM + HS_SG, na.rm = TRUE)
### Number Group within Group ----
#### nord_Order----
, nord_COET = dplyr::n_distinct(ORDER[ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### nfam_Order----
, nfam_Coleo = dplyr::n_distinct(FAMILY[ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, nfam_Ephem = dplyr::n_distinct(FAMILY[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, nfam_Odon = dplyr::n_distinct(FAMILY[ORDER == "ODONATA"]
, na.rm = TRUE)
, nfam_Trich = dplyr::n_distinct(FAMILY[ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### ngen_Order----
, ngen_Coleo = dplyr::n_distinct(GENUS[ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, ngen_Ephem = dplyr::n_distinct(GENUS[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, ngen_Odon = dplyr::n_distinct(GENUS[ORDER == "ODONATA"]
, na.rm = TRUE)
, ngen_Trich = dplyr::n_distinct(GENUS[ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### nfam_Family ----
# added next to nt_POET above for use with nt_POET_famBae
# so only code once
# , nfam_Baetidae = dplyr::n_distinct(FAMILY[EXCLUDE != TRUE
# & FAMILY == "BAETIDAE"]
# , na.rm = TRUE)
#### ngen_Family----
, ngen_Elmid = dplyr::n_distinct(GENUS[FAMILY == "ELMIDAE"]
, na.rm = TRUE)
### SPECIAL ####
# oddball or specialized metrics
# , ni_NonIns = sum(N_TAXA[CLASS==NA | CLASS!="INSECTA"], na.rm = TRUE)
# , ni_NonArach = sum(N_TAXA[CLASS==NA | CLASS!="ARACHNIDA"], na.rm = TRUE)
# , ni_NonDeca = sum(N_TAXA[ORDER==NA | ORDER!="DECAPODA"], na.rm = TRUE)
#
# , ni_clumpy = sum(N_TAXA[GENUS=="JUGA" & GENUS=="Rissoidea"], na.rm = TRUE)
# , ni_Nonclumpy = sum(N_TAXA[GENUS!="JUGA" & GENUS!="Rissoidea"], na.rm = TRUE)
#
# PacNW, NonIns_select
#This metric excludes Class INSECTA, Class ARACHNIDA and Order DECAPODA;
# and only includes Attribute IV, V, VI taxa.
, nt_NonInsArachDeca_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| ORDER != "DECAPODA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsArachDeca_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| ORDER != "DECAPODA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsArachDeca_BCG_att456 = 100 * nt_NonInsArachDeca_BCG_att456 / nt_total
# PacNW, NonIns_select_NonClump
# above but also non-clumpy
#clumpy' taxa (Juga [genus] and RISSOOIDEA [superfamily as Order] in PacNW);
#and it only includes Attribute IV, V, VI taxa.
, nt_NonInsArachDecaJugaRiss_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| (ORDER != "DECAPODA"
& ORDER != "RISSOOIDEA"))
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsArachDecaJugaRiss_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| (ORDER != "DECAPODA"
& ORDER != "RISSOOIDEA"))
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsArachDecaJugaRiss_BCG_att456 = 100 * nt_NonInsArachDecaJugaRiss_BCG_att456 / nt_total
, nt_NonInsTrombJuga_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "TROMBIDIFORMES")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsTrombJuga_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "TROMBIDIFORMES")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsTrombJuga_BCG_att456 = 100 * nt_NonInsTrombJuga_BCG_att456 / nt_total
, nt_oneind = dplyr::n_distinct(TAXAID[N_TAXA == 1
& EXCLUDE != TRUE]
, na.rm = TRUE)
, pt_oneind = 100 * nt_oneind / nt_total
, nt_airbreath = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& AIRBREATHER == TRUE]
, na.rm = TRUE)
, pi_airbreath = 100 * sum(N_TAXA[AIRBREATHER == TRUE]
, na.rm = TRUE) / ni_total
, pt_airbreath = 100 * nt_airbreath / nt_total
# NM BCG
, ni_total_300 = 100 * (ni_total / 300)
, nt_Mol_Non_BCG_att6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"
& (is.na(BCG_ATTR)
| BCG_ATTR != "6")]
, na.rm = TRUE)
# WY, add to match MetricScores.xlsx
, pi_EphemNoBaeTri_RFadj = NA_real_
, nt_volt_semi_RFadj = NA_real_
, nt_COETNoBraBaeHydTri_RFadj = NA_real_
, x_BCICTQa_RFadjB = NA_real_
#
, .groups = "drop_last")## met.val.dni_F
##met.val, DNI = TRUE----
met.val.dni_T <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
### totals----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
### DNI----
, nt_dni = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TAXAID == "DNI"]
, na.rm = TRUE)
, pi_dni = 100 * sum(N_TAXA[TAXAID == "DNI"]
, na.rm = TRUE) / ni_total
, pt_dni = 100 * nt_dni / nt_total
, .groups = "drop_last")## met.val.dni_T
## met.val, join----
cols2match <- c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS")
met_dni <- c("nt_dni", "pi_dni", "pt_dni")
met.val <- dplyr::left_join(met.val.dni_F
, met.val.dni_T[, c(cols2match, met_dni)])
}## IF ~ metric_subset
time_end2 <- Sys.time()
# difftime(time_end2, time_start2)
# dim(met.val)
#
# Clean Up ####
if (verbose == TRUE) {
debug_topic <- "clean up"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# replace NA with 0
#met.val[is.na(met.val)] <- 0
# but exclude SAMPLEID, INDEX_NAME INDEX_CLASS
# met.val <- met.val %>% dplyr::mutate(dplyr::across(where(is.numeric)
# , tidyr::replace_na
# , 0))
met.val <- as.data.frame(met.val)
met.val <- met.val %>% dplyr::mutate_if(is.numeric, tidyr::replace_na, 0)
# Crazy slow on tibble (several minutes) convert to data frame (< 2 seconds)
# met.val <- replace(is.na(met.val), 0)
# Marine Metrics
MetricNames_Marine <- c("nt_Capit"
, "nt_Caridea"
, "nt_Nereid"
, "nt_Nudib"
, "nt_Poly"
, "nt_PolyNoSpion"
, "nt_Spion"
, "pi_Amp"
, "pi_AmpHaust"
, "pi_Capit"
, "pi_Cirra"
, "pi_Clite"
, "pi_Haust"
, "pi_Hesion"
, "pi_Lucin"
, "pi_LucinTellin"
, "pi_Nereid"
, "pi_Nudib"
, "pi_Orbin"
, "pi_Poly"
, "pi_Spion"
, "pi_Spion2Poly"
, "pi_Tellin"
, "pi_Xanth"
, "pt_Nudib"
, "pt_Poly"
, "pt_PolyNoSpion"
, "pt_Spion"
, "rt_Amph"
, "rt_Bivalve"
, "rt_Capit"
, "rt_Car"
, "rt_Coleo"
, "rt_CruMol"
, "rt_Deca"
, "rt_Ephem"
, "rt_EPT"
, "rt_Gast"
, "rt_Isop"
, "rt_Nereid"
, "rt_Nudib"
, "rt_Oligo"
, "rt_Pleco"
, "rt_Poly"
, "rt_PolyNoSpion"
, "rt_Ptero"
, "rt_Spion"
, "rt_Trich"
, "rt_Tubif"
, "x_Becks_tv2"
)
## Subset ----
# # subset to only metrics specified by user
if (verbose == TRUE) {
debug_topic <- "subset"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(MetricNames)) {
# remove marine if MetrcNames not provided and boo.marine = false (default)
if (boo.marine == FALSE) {
met.val <- met.val[, !(names(met.val) %in% MetricNames_Marine)]
}## IF ~ boo.marine ~ END
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME",
"ni_total", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (verbose == TRUE) {
debug_topic <- "extra fields"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>%
dplyr::group_by(.dots = c("SAMPLEID", cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val)
, by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# df to report back
if (verbose == TRUE) {
debug_topic <- "return result"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
return(df.return)
}##FUNCTION.metric.values.bugs.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Fish
#'
#' @description Subfunction of metric.values for use with Fish.
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.fish <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, boo.Shiny
, verbose) {
# QC
boo_QC <- FALSE
if (boo_QC) {
myDF <- BioMonTools::data_fish_MBSS
MetricNames <- NULL
boo.Adjust <- FALSE
cols2keep <- NULL
boo.Shiny <- FALSE
verbose <- TRUE
}## IF ~ boo_QC
time_start <- Sys.time()
# not carrying over from previous?!
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "FISH"
boo_debug_sub <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 12
# global variable bindings ----
SAMPLEID <- INDEX_NAME <- INDEX_CLASS <- TAXAID <- N_TAXA <- NATIVE <-
HYBRID <- TYPE <- TROPHIC <- SILT <- TOLER <- N_ANOMALIES <- GENUS <-
FAMILY <- SAMP_WIDTH_M <- SAMP_LENGTH_M <- NULL
TROPHIC_GE <- TROPHIC_HB <- TROPHIC_IS <- TROPHIC_IV <- TROPHIC_OM <-
TROPHIC_TC <- NULL
ni_total <- x_Shan_e <- nt_total <- x_Evenness <- length_m <-
ni_natnonhybridnonmf <- ni_natnonhybridnonmfnonlepomis <- NULL
BCG_ATTR <- NULL
CONNECTIVITY <- SCC <- nt_AmmEthPerc <- nt_AmmEthPerc_Cott_Notur <-
nt_Cato <- nt_Cent <- nt_natCent <- nt_Cott <- nt_Cyprin <- nt_Ictal <-
nt_Lepomis <- nt_native <- nt_nonnative <- nt_Notur <- nt_Salm <-
nt_connect <- nt_scc <- TROPHIC_DE <- TROPHIC_PL <- nt_detritivore <-
nt_herbivore <- nt_omnivore <- nt_planktivore <- nt_topcarn <- area_m2 <-
ni_natnonhybridnonmfnonLepomis <- SAMP_BIOMASS <- ni_dom02 <- ni_dom03 <-
ni_dom04 <- ni_dom05 <- ni_dom06 <- ni_dom07 <- ni_dom08 <- ni_dom09 <-
ni_dom10 <- nt_BCG_att12 <- nt_BCG_att123 <- nt_BCG_att12346b <-
nt_BCG_att1236b <- nt_BCG_att2 <- nt_BCG_att2native <- nt_BCG_att23_scc <-
nt_BCG_att3 <- nt_BCG_att3native <- nt_BCG_att4 <- nt_BCG_att4native <-
nt_BCG_att5 <- nt_BCG_att5native <- nt_BCG_attNA <- TI_CORECOLD <-
TI_COLD <- TI_COOL <- TI_WARM <- TI_EURY <- TI_NA <- nt_ti_corecold <-
nt_ti_cold <- nt_ti_cool <- nt_ti_warm <- nt_ti_eury <- nt_ti_na <-
nt_ti_corecold_cold <- nt_ti_cool_warm <- ELEVATION_LOW <- ELEVATION_HIGH <-
GRADIENT_LOW <- GRADIENT_MOD <- GRADIENT_HIGH <- WSAREA_S <- WSAREA_M <-
WSAREA_L <- WSAREA_XL <- REPRO_BCAST <- REPRO_NS <- REPRO_NC <-
REPRO_BEAR <- REPRO_MIG <- HABITAT_B <- HABITAT_W <- nt_habitat_b <-
nt_habitat_w <- NULL
nt_natcoldwater <- nt_serialspawner <- nt_simplelithophil <- nt_tv_sens <-
nt_tv_senscoldwater <- nt_tv_toler <- nt_tv_vtoler <- nt_beninsct_notoler <-
pt_gen <- nt_gen <- nt_insectivore_notoler <- nt_darterscultpinsucker <-
nt_pioneer <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC ####
# Remove Non-Target Taxa
#myDF <- myDF[myDF[,"NonTarget"]==0,] # not relevant for fish
## QC, Missing Cols ----
if (verbose == TRUE) {
# 1
debug_topic <- "QC, required cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
, "FAMILY", "GENUS"
, "TYPE", "TOLER", "NATIVE", "TROPHIC", "SILT"
, "BCG_ATTR", "THERMAL_INDICATOR"
, "HABITAT", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR"
, "REPRODUCTION", "HABITAT", "CONNECTIVITY", "SCC"
, "BCG_ATTR2")
col.req_logical <- c("EXCLUDE", "HYBRID")
col.req_numeric <- c("N_TAXA", "N_ANOMALIES", "SAMP_BIOMASS", "DA_MI2"
, "SAMP_WIDTH_M", "SAMP_LENGTH_M", "TOLVAL2"
)
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
# col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "EXCLUDE"
# , "N_ANOMALIES", "SAMP_BIOMASS"
# , "INDEX_NAME", "INDEX_CLASS"
# , "DA_MI2", "SAMP_WIDTH_M", "SAMP_LENGTH_M"
# , "TYPE", "TOLER", "NATIVE", "TROPHIC", "SILT"
# , "FAMILY", "GENUS", "HYBRID", "BCG_ATTR", "THERMAL_INDICATOR"
# , "ELEVATION_ATTR", "GRADIENT_ATTR", "WSAREA_ATTR"
# , "REPRODUCTION", "HABITAT", "CONNECTIVITY", "SCC"
# )
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {##IF.num.col.req.missing.START
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the NATIVE field is missing all native related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" ", myPrompt.01, myPrompt.02, " ", myPrompt.03, myPrompt.04
, myPrompt.05, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive and boo.Shiny
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
myDF[, col.req.missing] <- NA
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Exclude"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "EXCLUDE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {
warn1 <- "EXCLUDE column does not have any TRUE values."
warn2 <- "This is common with fish samples."
warn3 <- "Valid values are TRUE or FALSE."
warn4 <- "Other values are not recognized"
msg <- paste(warn1, warn2, warn3, warn4, sep = "\n")
message(msg)
}##IF.Exclude.T.END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging ----
if (verbose == TRUE) {
# 2
debug_topic <- "Munge, values to upper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Column Values to UPPER case for met.val below
col2upper <- c("TAXAID" ,"FAMILY", "GENUS", "TYPE", "TOLER", "NATIVE"
, "TROPHIC", "THERMAL_INDICATOR", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR", "REPRODUCTION", "HABITAT"
, "CONNECTIVITY", "SCC", "BCG_ATTR", "BCG_ATTR2")
for (i in col2upper) {
if (i %in% names(myDF)) {
myDF[, i] <- toupper(myDF[, i])
}## IF ~ i %in%
}##FOR ~ i col2upper
# Add extra columns for some fields
if (verbose == TRUE) {
# 4
debug_topic <- "Munge, TF"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "GE, IV" is both "GE" and "IV"
## HABITAT ----
if (!"HABITAT" %in% names(myDF)) {
myDF[, "HABITAT"] <- NA
}## IF ~ HABITAT
# Remove white space
myDF[, "HABITAT"] <- gsub(" ", "", myDF[, "HABITAT"])
# code new columns
myDF[, "HABITAT_B"] <- grepl("B", myDF[,"HABITAT"])
myDF[, "HABITAT_F"] <- grepl("F", myDF[,"HABITAT"]) # Fluvial
# W (MOD b/c of MN CW and CWN)
myDF[, "HABITAT_W"] <- grepl("^W$|^W,|,W$|,W,", myDF[,"HABITAT"])
# MN
myDF[, "HABITAT_CW"] <- grepl("^CW$|^CW,|CW$|,CW,", myDF[,"HABITAT"]) # CW
myDF[, "HABITAT_CWN"] <- grepl("CWN", myDF[,"HABITAT"]) # Coldwater, Native
myDF[, "HABITAT_HW_noT"] <- grepl("HW-T", myDF[,"HABITAT"]) # Headwater Specialist, no Tolerant
myDF[, "HABITAT_WE_noT"] <- grepl("WE-T", myDF[,"HABITAT"]) # Wetland, no Tolerant
## REPRODUCTION ----
if (!"REPRODUCTION" %in% names(myDF)) {
myDF[, "REPRODUCTION"] <- NA
}## IF ~ REPRODUCTION
# Remove white space
myDF[, "REPRODUCTION"] <- gsub(" ", "", myDF[, "REPRODUCTION"])
# code new columns
myDF[, "REPRO_BCAST"] <- grepl("BROADCASTER", myDF[,"REPRODUCTION"])
myDF[, "REPRO_NS"] <- grepl("SIMPLE NEST", myDF[,"REPRODUCTION"])
myDF[, "REPRO_NC"] <- grepl("COMPLEX NEST", myDF[,"REPRODUCTION"])
myDF[, "REPRO_BEAR"] <- grepl("BEARER", myDF[,"REPRODUCTION"])
myDF[, "REPRO_MIG"] <- grepl("MIGRATORY", myDF[,"REPRODUCTION"])
myDF[, "REPRO_LITH"] <- grepl("LITHOPHIL", myDF[,"REPRODUCTION"])
# MN
myDF[, "REPRO_MA2"] <- grepl("MA<2", myDF[,"REPRODUCTION"]) # Mature Age < 2
myDF[, "REPRO_MA3_noT"] <- grepl("MA>3-T", myDF[,"REPRODUCTION"]) # Mature Age > 3, no Tolerant
myDF[, "REPRO_NE"] <- grepl("NE", myDF[,"REPRODUCTION"]) # NonLithophilic Nester
myDF[, "REPRO_SER"] <- grepl("SER", myDF[,"REPRODUCTION"]) # Serial Spawner
myDF[, "REPRO_SILI"] <- grepl("SILI", myDF[,"REPRODUCTION"]) # Simple Lithophil
## THERMAL_INDICATOR----
if (!"THERMAL_INDICATOR" %in% names(myDF)) {
myDF[, "THERMAL_INDICATOR"] <- NA
}## IF ~ THERMAL_INDICATOR
# Remove white space
myDF[, "THERMAL_INDICATOR"] <- gsub(" ", "", myDF[, "THERMAL_INDICATOR"])
# code new columns
myDF[, "TI_CORECOLD"] <- grepl("COREC", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_COLD"] <- grepl("COLD", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_COOL"] <- grepl("COOL", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_WARM"] <- grepl("WARM", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_EURY"] <- grepl("EURYTHERMAL", myDF[,"THERMAL_INDICATOR"])
# exact matches only
myDF[, "TI_NA"] <- is.na(myDF[, "THERMAL_INDICATOR"])
## TOLER ----
if (!"TOLER" %in% names(myDF)) {
myDF[, "TOLER"] <- NA
}## IF ~ TOLER
# Remove white space
myDF[, "TOLER"] <- gsub(" ", "", myDF[, "TOLER"])
# code new columns
myDF[, "TOLER_TOLERANT"] <- grepl("TOLERANT", myDF[, "TOLER"]) # NOT USED
myDF[, "TOLER_INTOLERANT"] <- grepl("INTOLERANT", myDF[,"TOLER"]) # NOT USED
# MN
myDF[, "TOLER_ICW"] <- grepl("ICW", myDF[,"TOLER"])
myDF[, "TOLER_I"] <- grepl("^I$|^I,|,I$|,I,", myDF[,"TOLER"])
myDF[, "TOLER_ICW"] <- grepl("ICW", myDF[,"TOLER"])
myDF[, "TOLER_S"] <- grepl("^S$|^S,|,S$|,S,", myDF[,"TOLER"])
myDF[, "TOLER_SCW"] <- grepl("SCW", myDF[,"TOLER"])
myDF[, "TOLER_T"] <- grepl("^T$|^T,|,T$|,T,", myDF[,"TOLER"])
myDF[, "TOLER_TCW"] <- grepl("TCW", myDF[,"TOLER"])
myDF[, "TOLER_VT"] <- grepl("VT", myDF[,"TOLER"])
## TROPHIC ----
if (!"TROPHIC" %in% names(myDF)) {
myDF[, "TROPHIC"] <- NA
}## IF ~ TROPHIC
# Remove white space
myDF[, "TROPHIC"] <- gsub(" ", "", myDF[, "TROPHIC"])
# code new columns
myDF[, "TROPHIC_GE"] <- grepl("GE", myDF[, "TROPHIC"]) # Generalist
myDF[, "TROPHIC_HB"] <- grepl("HB|HE", myDF[, "TROPHIC"]) # Herbivore
myDF[, "TROPHIC_IS"] <- grepl("IS", myDF[, "TROPHIC"]) # Insectivore
myDF[, "TROPHIC_IV"] <- grepl("^IV$|^IV,|,IV$|,IV,", myDF[, "TROPHIC"]) # Invertivore
myDF[, "TROPHIC_OM"] <- grepl("OM", myDF[, "TROPHIC"]) # Omnivore
myDF[, "TROPHIC_TC"] <- grepl("^TC$|^TC,|,TC$|,TC,", myDF[, "TROPHIC"]) # Top Carnivore
myDF[, "TROPHIC_DE"] <- grepl("^DE$|^DE,|,DE$|,DE,", myDF[, "TROPHIC"]) # Detritivore (mod for DEM)
myDF[, "TROPHIC_PL"] <- grepl("PL", myDF[, "TROPHIC"]) # Planktivore
myDF[, "TROPHIC_PI"] <- grepl("PI", myDF[, "TROPHIC"]) # Piscivore
myDF[, "TROPHIC_IV_TC"] <- grepl("IV_TC", myDF[, "TROPHIC"]) # Invertivore and Top Carnivore
# MN
myDF[, "TROPHIC_BI_noT"] <- grepl("BI-T", myDF[, "TROPHIC"]) # Benthic Insectivore, no Tolerant
myDF[, "TROPHIC_IN_noT"] <- grepl("IN-T", myDF[, "TROPHIC"]) # Insectivore, no Tolerant
myDF[, "TROPHIC_IN_CYP"] <- grepl("INCYP", myDF[, "TROPHIC"]) # Insectivorous Cyprinidae
myDF[, "TROPHIC_DEM"] <- grepl("DEM", myDF[, "TROPHIC"]) # Detritivore Minor
## TYPE ----
if (!"TYPE" %in% names(myDF)) {
myDF[, "TYPE"] <- NA
}## IF ~ TYPE
# Remove white space
myDF[, "TYPE"] <- gsub(" ", "", myDF[, "TYPE"])
# code new columns
# Type is a catch all column so need to be specific in pattern match
# MN, Composition
myDF[, "TYPE_DSS"] <- grepl("^DSS$|^DSS,|,DSS$|,DSS,", myDF[,"TYPE"])
myDF[, "TYPE_DS"] <- grepl("^DS$|^DS,|,DS$|,DS,", myDF[,"TYPE"])
myDF[, "TYPE_EX"] <- grepl("^EX$|^EX,|,EX$|,EX,", myDF[,"TYPE"])
myDF[, "TYPE_MIN_noT"] <- grepl("^MIN-T$|^MIN-T,|,MIN-T$|,MIN-T,", myDF[,"TYPE"])
myDF[, "TYPE_PERC"] <- grepl("^PERC$|^PERC,|,PERC$|,PERC,", myDF[,"TYPE"])
# MN, Life History
myDF[, "TYPE_PI"] <- grepl("^PI$|^PI,|,PI$|,PI,", myDF[,"TYPE"])
myDF[, "TYPE_SL"] <- grepl("^SL$|^SL,|,SL$|,SL,", myDF[,"TYPE"])
# MN, Schooling
myDF[, "TYPE_SCHOOL"] <- grepl("^SCH$|^SCH,|,SCH$|,SCH,", myDF[,"TYPE"])
# MN, Brook Trout
myDF[, "TYPE_BROOKTROUT"] <- grepl("^BKT$|^BKT,|,BKT$|,BKT,", myDF[,"TYPE"])
# GP, Salt
myDF[, "TYPE_SALT"] <- grepl("SALT", myDF[, "TYPE"])
# GP, NPL
myDF[, "TYPE_NPL"] <- grepl("NPL", myDF[, "TYPE"])
## ELEVATION_ATTR ----
if (!"ELEVATION_ATTR" %in% names(myDF)) {
myDF[, "ELEVATION_ATTR"] <- NA
}## IF ~ ELEVATION_ATTR
# Remove white space
myDF[, "ELEVATION_ATTR"] <- gsub(" ", "", myDF[, "ELEVATION_ATTR"])
# code new columns
myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"]
myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"]
## GRADIENT_ATTR----
if (!"GRADIENT_ATTR" %in% names(myDF)) {
myDF[, "GRADIENT_ATTR"] <- NA
}## IF ~ GRADIENT_ATTR
# Remove white space
myDF[, "GRADIENT_ATTR"] <- gsub(" ", "", myDF[, "GRADIENT_ATTR"])
# code new columns
myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"]
## WSAREA_ATTR ----
if (!"WSAREA_ATTR" %in% names(myDF)) {
myDF[, "WSAREA_ATTR"] <- NA
}## IF ~ WSAREA_ATTR
# Remove white space
myDF[, "WSAREA_ATTR"] <- gsub(" ", "", myDF[, "WSAREA_ATTR"])
# code new columns
myDF[, "WSAREA_S"] <- "SMALL" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_M"] <- "MEDIUM" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_L"] <- "LARGE" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_XL"] <- "XLARGE" == myDF[, "WSAREA_ATTR"]
## Create Dominant N ####
if (verbose == TRUE) {
# 4
debug_topic <- "Munge, Dom"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# DF for dom so same taxa get combined
myDF_dom <- dplyr::summarise(dplyr::group_by(myDF
, INDEX_NAME
, INDEX_CLASS
, SAMPLEID
, TAXAID
, TYPE_SCHOOL)
, N_TAXA = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# MN, add TYPE_SCHOOL, 20240601
# Create df for Top N (without ties)
#
df.dom01 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom02 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom03 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 3)
df.dom04 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 4)
df.dom05 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 5)
df.dom06 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 6)
df.dom07 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 7)
df.dom08 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 8)
df.dom09 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 9)
df.dom10 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 10)
# MN
df_dom01_ExclSchool <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(TYPE_SCHOOL != TRUE) %>%
dplyr::filter(dplyr::row_number() <= 1)
df_dom02_ExclSchool <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(TYPE_SCHOOL != TRUE) %>%
dplyr::filter(dplyr::row_number() <= 2)
# Summarise Top N
df.dom01.sum <- dplyr::summarise(dplyr::group_by(df.dom01
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02.sum <- dplyr::summarise(dplyr::group_by(df.dom02
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom03.sum <- dplyr::summarise(dplyr::group_by(df.dom03
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom03 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom04.sum <- dplyr::summarise(dplyr::group_by(df.dom04
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom04 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom05.sum <- dplyr::summarise(dplyr::group_by(df.dom05
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom05 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom06.sum <- dplyr::summarise(dplyr::group_by(df.dom06
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom06 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom07.sum <- dplyr::summarise(dplyr::group_by(df.dom07
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom07 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom08.sum <- dplyr::summarise(dplyr::group_by(df.dom08
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom08 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom09.sum <- dplyr::summarise(dplyr::group_by(df.dom09
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom09 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom10.sum <- dplyr::summarise(dplyr::group_by(df.dom10
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom10 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# MN
df_dom01_ExclSchool_sum <- dplyr::summarise(dplyr::group_by(df_dom01_ExclSchool
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_ExclSchool = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df_dom02_ExclSchool_sum <- dplyr::summarise(dplyr::group_by(df_dom02_ExclSchool
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02_ExclSchool = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# Add column of domN to main DF
myDF <- merge(myDF, df.dom01.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom03.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom04.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom05.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom06.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom07.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom08.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom09.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom10.sum, all.x = TRUE)
myDF <- merge(myDF, df_dom01_ExclSchool_sum, all.x = TRUE)
myDF <- merge(myDF, df_dom02_ExclSchool_sum, all.x = TRUE)
# Clean up extra Dom data frames
rm(myDF_dom)
rm(df.dom01)
rm(df.dom02)
rm(df.dom03)
rm(df.dom04)
rm(df.dom05)
rm(df.dom06)
rm(df.dom07)
rm(df.dom08)
rm(df.dom09)
rm(df.dom10)
rm(df_dom01_ExclSchool)
rm(df_dom02_ExclSchool)
rm(df.dom01.sum)
rm(df.dom02.sum)
rm(df.dom03.sum)
rm(df.dom04.sum)
rm(df.dom05.sum)
rm(df.dom06.sum)
rm(df.dom07.sum)
rm(df.dom08.sum)
rm(df.dom09.sum)
rm(df.dom10.sum)
rm(df_dom01_ExclSchool_sum)
rm(df_dom02_ExclSchool_sum)
## N_Anomalies ----
if (verbose == TRUE) {
# 5
debug_topic <- "Munge, anomalies"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Munge N_Anomalies, NA to 0
myDF[, "N_ANOMALIES"] <- as.numeric(myDF[, "N_ANOMALIES"])
myDF[is.na(myDF[, "N_ANOMALIES"]), "N_ANOMALIES"] <- 0
# By taxon or sample total
# Data set up to have anomalies by taxon.
# But some report as sample total.
# This routine redistributes values proportionally to all taxa
# *IF* all are the same value
# Cases of same number of anomalies for all taxa should be rare but possible
stats_anom <- myDF %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::summarize(n = dplyr::n()
, n_distinct = dplyr::n_distinct(N_ANOMALIES, na.rm = TRUE)
, mean = mean(N_ANOMALIES, na.rm = TRUE)
, sd = stats::sd(N_ANOMALIES, na.rm = TRUE)
, sum = sum(N_ANOMALIES, na.rm = TRUE))
stats_anom[, "SUM_ANOMALIES"] <- stats_anom[, "mean"] / stats_anom[, "n"]
# make change; n > 1 & n_distinct == 1
stats_anom$MOD_ANOMALIES <- ifelse(stats_anom$n > 1 &
stats_anom$n_distinct == 1, TRUE, FALSE)
# add back to myDF
myDF <- merge(myDF, stats_anom[, c("SAMPLEID"
, "SUM_ANOMALIES"
, "MOD_ANOMALIES")]
, all.x = TRUE)
myDF[myDF$MOD_ANOMALIES == TRUE, "N_ANOMALIES"] <- myDF[myDF$MOD_ANOMALIES == TRUE
, "SUM_ANOMALIES"]
# Metric Calc ####
if (verbose == TRUE) {
# 6
debug_topic <- "Calc, metrics"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# code above is different than benthos
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF, SAMPLEID, INDEX_NAME
, INDEX_CLASS, SAMP_WIDTH_M
, SAMP_LENGTH_M)
, .groups = "drop_last"
#
# MBSS 2005, 11 metrics
# (can do metrics as one step but MBSS output has
# numerator so will get that as well)
#
# when invoke a "x != abc" need to include "| is.na(x)"
# unless all "x" are populated (e.g., TRUE or FALSE)
## Individuals ####
# individuals, total
, ni_total = sum(N_TAXA, na.rm = TRUE)
, ni_total_notoler = sum(N_TAXA[TOLER != "TOLERANT" | is.na(TOLER)], na.rm = TRUE)
, ni_natnonhybridnonmf = sum(N_TAXA[NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID)) &
(TYPE != "MOSQUITOFISH" | is.na(TYPE))], na.rm = TRUE)
, ni_natnonhybridnonmfnonLepomis = sum(N_TAXA[NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID)) &
(TYPE != "MOSQUITOFISH" | is.na(TYPE)) &
(GENUS != "LEPOMIS" | is.na(GENUS))], na.rm = TRUE)
#
## Percent Individuals ####
, pi_AmmEthPerc = 100 * sum(N_TAXA[GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"], na.rm = TRUE) / ni_total
, pi_AmmEthPerc_Cott_Notur = 100 * sum(N_TAXA[(GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"
| GENUS == "NOTURUS")
| FAMILY == "COTTIDAE"]
, na.rm = TRUE) / ni_total
# % Round-Bodied Suckers
, pi_rbs = 100 * sum(N_TAXA[TYPE == "RBS"], na.rm = TRUE) / ni_total
, pi_brooktrout = 100 * sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) / ni_total
, pi_brooktrout_wild = 100 * sum(N_TAXA[TAXAID == "BROOK TROUT, WILD"], na.rm = TRUE) / ni_total
, pi_Cato = 100 * sum(N_TAXA[FAMILY == "CATOSTOMIDAE"], na.rm = TRUE) / ni_total
, pi_Cent = 100 * sum(N_TAXA[FAMILY == "CENTRARCHIDAE"], na.rm = TRUE) / ni_total
, pi_natCent = 100 * sum(N_TAXA[NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE) / ni_total
, pi_Cott = 100 * sum(N_TAXA[FAMILY == "COTTIDAE"], na.rm = TRUE) / ni_total
, pi_Cyprin = 100 * sum(N_TAXA[FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
, pi_Ictal = 100 * sum(N_TAXA[FAMILY == "ICTALURIDAE"], na.rm = TRUE) / ni_total
, pi_native = 100 * sum(N_TAXA[NATIVE == "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative = 100 * sum(N_TAXA[is.na(NATIVE) | NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative_NotNativeNotNA = 100 * sum(N_TAXA[NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative_OnlyNonNative = 100 * sum(N_TAXA[NATIVE == "NON-NATIVE"], na.rm = TRUE) / ni_total
, pi_Notur = 100 * sum(N_TAXA[GENUS == "NOTURUS"], na.rm = TRUE) / ni_total
, pi_sculpin = 100 * sum(N_TAXA[TYPE == "SCULPIN"], na.rm = TRUE) / ni_total
, pi_Lepomis = 100 * sum(N_TAXA[GENUS == "LEPOMIS"], na.rm = TRUE) / ni_total
, pi_Salm = 100 * sum(N_TAXA[FAMILY == "SALMONIDAE"], na.rm = TRUE) / ni_total
, pi_trout = 100 * sum(N_TAXA["TROUT" %in% TYPE], na.rm = TRUE) / ni_total
, pi_brooktrout_BCG_att6 = 100 * (sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "6"], na.rm = TRUE)) / ni_total
, pi_connect = 100 * sum(N_TAXA[CONNECTIVITY == TRUE], na.rm = TRUE) / ni_total
, pi_scc = 100 * sum(N_TAXA[SCC == TRUE], na.rm = TRUE) / ni_total
, pi_brooktrout2brooktrout_BCG_att6 = 100 *
sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) /
(sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "6"], na.rm = TRUE))
# benthic fluvial specialist
, pi_bfs = 100 * sum(N_TAXA[(TYPE == "BENTHIC" & TROPHIC_IV == TRUE) |
TYPE == "RBS" | TYPE == "SMM"], na.rm = TRUE) / ni_total
#
## Number of Taxa ####
# account for "NONE" in nt_total, should be the only 0 N_TAXA
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & N_TAXA > 0], na.rm = TRUE)
#, nt_benthic=dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TYPE == "DARTER" | TYPE == "SCULPIN" | TYPE == "MADTOM" | TYPE == "LAMPREY"])
, nt_benthic = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TYPE == "BENTHIC"], na.rm = TRUE)
, nt_AmmEthPerc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA")], na.rm = TRUE)
, nt_AmmEthPerc_Cott_Notur = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"
| GENUS == "NOTURUS")
| FAMILY == "COTTIDAE"]
, na.rm = TRUE)
, nt_Cato = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CATOSTOMIDAE"], na.rm = TRUE)
, nt_Cent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_natCent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_Cott = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "COTTIDAE"], na.rm = TRUE)
, nt_Cyprin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_natCyprin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_Lepomis = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GENUS == "LEPOMIS"], na.rm = TRUE)
, nt_native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & N_TAXA > 0], na.rm = TRUE)
, nt_nonnative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(NATIVE) | NATIVE != "NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nonnative_NotNativeNotNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (NATIVE != "NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nonnative_OnlyNonNative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (NATIVE == "NON-NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nativenonhybrid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID))], na.rm = TRUE)
, nt_Notur = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GENUS == "NOTURUS"], na.rm = TRUE)
, nt_Ictal = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "ICTALURIDAE"], na.rm = TRUE)
, nt_natsunfish = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & TYPE == "SUNFISH"], na.rm = TRUE)
, nt_natCent_sunfish = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
(TYPE == "SUNFISH" | TYPE == "CENTRARCHIDAE")], na.rm = TRUE)
, nt_natCent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_natinsctCypr = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
TROPHIC_IS == TRUE & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_natrbs = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & TYPE == "RBS"], na.rm = TRUE)
, nt_Petro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "PETROMYZONTIDAE"], na.rm = TRUE)
, nt_Salm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "SALMONIDAE"], na.rm = TRUE)
, nt_connect = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & CONNECTIVITY == TRUE], na.rm = TRUE)
, nt_scc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & SCC == TRUE], na.rm = TRUE)
, nt_beninsct_nows_nobg = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TROPHIC_IS == TRUE
& (TAXAID != "CATOSTOMUS COMMERSONII"
| TAXAID != "LEPOMIS MACROCHIRUS"
| is.na(TAXAID))
], na.rm = TRUE)
, nt_trout_sunfish_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ("TROUT" %in% TYPE
| TYPE == "SUNFISH")
& (TOLER != "TOLERANT"
| is.na(TOLER))
], na.rm = TRUE)
# , nt_beninsct_nows_nobg = NA
# , nt_trout_sunfish_notoler = NA
# , pi_pisc_noae = NA
## Percent of Taxa ----
, pt_AmmEthPerc = 100 * nt_AmmEthPerc / nt_total
, pt_AmmEthPerc_Cott_Notur = 100 * nt_AmmEthPerc_Cott_Notur / nt_total
, pt_Cato = 100 * nt_Cato / nt_total
, pt_Cent = 100 * nt_Cent / nt_total
, pt_natCent = 100 * nt_natCent / nt_total
, pt_Cott = 100 * nt_Cott / nt_total
, pt_Cyprin = 100 * nt_Cyprin / nt_total
, pt_Ictal = 100 * nt_Ictal / nt_total
, pt_Lepomis = 100 * nt_Lepomis / nt_total
, pt_native = 100 * nt_native / nt_total
, pt_nonnative = 100 * nt_nonnative / nt_total
, pt_nonnative_NotNativeNotNA = 100 * nt_nonnative_NotNativeNotNA / nt_total
, pt_nonnative_OnlyNonNative = 100 * nt_nonnative_OnlyNonNative / nt_total
, pt_Notur = 100 * nt_Notur / nt_total
, pt_Salm = 100 * nt_Salm / nt_total
, pt_connect = 100 * nt_connect / nt_total
, pt_scc = 100 * nt_scc / nt_total
## Trophic ####
### Trophic, nt----
, nt_beninvert = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE == "BENTHIC"
& TROPHIC_IV == TRUE]
, na.rm = TRUE)
, nt_habitat_beninvert = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV == TRUE
& HABITAT_B == TRUE]
, na.rm = TRUE)
, nt_detritivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_DE == TRUE]
, na.rm = TRUE)
, nt_herbivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_HB == TRUE]
, na.rm = TRUE)
, nt_invertivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV == TRUE]
, na.rm = TRUE)
, nt_inverttopcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV_TC == TRUE]
, na.rm = TRUE)
, nt_omnivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_OM == TRUE]
, na.rm = TRUE)
, nt_planktivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PL == TRUE
], na.rm = TRUE)
, nt_topcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_TC == TRUE]
, na.rm = TRUE)
, nt_piscivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PI == TRUE]
, na.rm = TRUE)
### Trophic, pi----
# % Lithophilic spawners
, pi_lithophil = 100 * sum(N_TAXA[SILT == TRUE], na.rm = TRUE) / ni_total
, pi_habitat_beninvert = 100 * sum(N_TAXA[TROPHIC_IV == TRUE
& HABITAT_B == TRUE], na.rm = TRUE) / ni_total
, pi_detritivore = 100 * sum(N_TAXA[TROPHIC_DE == TRUE], na.rm = TRUE) / ni_total
# % gen, omn, invert
, pi_gen = 100 * sum(N_TAXA[TROPHIC_GE == TRUE], na.rm = TRUE) / ni_total
, pi_genherb = 100 * sum(N_TAXA[TROPHIC_GE == TRUE | TROPHIC_HB == TRUE], na.rm = TRUE) / ni_total
, pi_genomninvrt = 100 * sum(N_TAXA[TROPHIC_GE == TRUE | TROPHIC_OM == TRUE | TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
, pi_herbivore = 100 * sum(N_TAXA[TROPHIC_HB == TRUE], na.rm = TRUE) / ni_total
, pi_insectivore = 100 * sum(N_TAXA[TROPHIC_IS == TRUE], na.rm = TRUE) / ni_total
, pi_insctCypr = 100 * sum(N_TAXA[TROPHIC_IS == TRUE &
FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
, pi_invertivore = 100 * sum(N_TAXA[TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
, pi_inverttopcarn = 100 * sum(N_TAXA[TROPHIC_IV_TC == TRUE], na.rm = TRUE) / ni_total
, pi_omnivore = 100 * sum(N_TAXA[TROPHIC_OM == TRUE], na.rm = TRUE) / ni_total
, pi_planktivore = 100 * sum(N_TAXA[TROPHIC_PL == TRUE], na.rm = TRUE) / ni_total
, pi_topcarn = 100 * sum(N_TAXA[TROPHIC_TC == TRUE], na.rm = TRUE) / ni_total
, pi_trout = 100 * sum(N_TAXA["TROUT" %in% TYPE], na.rm = TRUE) / ni_total
, pi_pisc_noae = 100 * sum(N_TAXA[TYPE == "PISCIVORE"
& (TAXAID != "ANGUILLA ROSTRATA"
| is.na(TAXAID))], na.rm = TRUE) / ni_total
### Trophic, pt ----
, pt_habitat_beninvert = 100 * nt_habitat_beninvert / nt_total
, pt_detritivore = 100 * nt_detritivore / nt_total
, pt_herbivore = 100 * nt_herbivore / nt_total
, pt_invertivore = 100 * nt_invertivore / nt_total
, pt_inverttopcarn = 100 * nt_inverttopcarn / nt_total
, pt_omnivore = 100 * nt_omnivore / nt_total
, pt_planktivore = 100 * nt_planktivore / nt_total
, pt_topcarn = 100 * nt_topcarn / nt_total
#
## Tolerance ####
, nt_tv_intol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TOLER == "INTOLERANT"], na.rm = TRUE)
, nt_tv_intolhwi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (TOLER == "INTOLERANT" |
TOLER == "HWI")], na.rm = TRUE)
, pi_tv_toler = 100 * sum(N_TAXA[TOLER == "TOLERANT"], na.rm = TRUE) / ni_total
#
## Indices ####
# Shannon-Weiner
#, x_Shan_Num= -sum(log(N_TAXA / ni_total)), na.rm = TRUE)
#, x_Shan_e=x_Shan_Num/log(exp(1))
, x_Shan_e = -sum((N_TAXA / ni_total)*log((N_TAXA / ni_total)), na.rm = TRUE)
, x_Shan_2 = x_Shan_e/log(2)
, x_Shan_10 = x_Shan_e/log(10)
, x_Evenness = x_Shan_e/log(nt_total)
, x_Evenness100_ni99gt = ifelse(ni_total < 100, 1, x_Evenness * 100)
#
## Other ----
, length_m = max(SAMP_LENGTH_M, na.rm = TRUE)
, area_m2 = max(SAMP_WIDTH_M, na.rm = TRUE) * length_m
### Abund / sq meter
, ni_m2 = ni_total / area_m2 #/(StWidAvg*StLength)
, ni_200m = 200 * ni_total / length_m
, ni_natnonhybridnonmf_200m = 200 * ni_natnonhybridnonmf / length_m
, ni_natnonhybridnonmfnonLepomis_200m = 200 * ni_natnonhybridnonmfnonLepomis / length_m
# biomass per square meter (assumes sample not individual biomass)
, biomass_m2 = max(SAMP_BIOMASS, na.rm = TRUE) / area_m2 #/(StWidAvg*StLength)
### Anomalies
, pi_anomalies = 100 * sum(N_ANOMALIES, na.rm = TRUE) / ni_total
, pi_delt = 100 * sum(N_ANOMALIES, na.rm = TRUE) / ni_total
## Dominant N ####
## uses previously defined values added to myDF
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
, pi_dom03 = 100 * max(ni_dom03, na.rm = TRUE) / ni_total
, pi_dom04 = 100 * max(ni_dom04, na.rm = TRUE) / ni_total
, pi_dom05 = 100 * max(ni_dom05, na.rm = TRUE) / ni_total
, pi_dom06 = 100 * max(ni_dom06, na.rm = TRUE) / ni_total
, pi_dom07 = 100 * max(ni_dom07, na.rm = TRUE) / ni_total
, pi_dom08 = 100 * max(ni_dom08, na.rm = TRUE) / ni_total
, pi_dom09 = 100 * max(ni_dom09, na.rm = TRUE) / ni_total
, pi_dom10 = 100 * max(ni_dom10, na.rm = TRUE) / ni_total
## BCG ####
### BCG, nt ----
, nt_BCG_att1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1"]
, na.rm = TRUE)
, nt_BCG_att12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG2_att123b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR2 == "3_BETTER")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG2_att1234b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att1236 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att1236b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6B")]
, na.rm = TRUE)
, nt_BCG_att12346 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att12346b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6B")]
, na.rm = TRUE)
, nt_BCG_att1i236i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "2"]
, na.rm = TRUE)
, nt_BCG_att2native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "2"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att23_scc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3")
& SCC == TRUE]
, na.rm = TRUE)
, nt_BCG_att3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "3"]
, na.rm = TRUE)
, nt_BCG_att3native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "3"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "4"]
, na.rm = TRUE)
, nt_BCG_att4native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "4"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att4b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_BCG_att4w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE)
, nt_BCG_att4w5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "5"]
, na.rm = TRUE)
, nt_BCG_att5native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "5"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att55a6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att55a6a = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE)
, nt_BCG_att56t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_att6i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6I"]
, na.rm = TRUE)
, nt_BCG_att6m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6M"]
, na.rm = TRUE)
, nt_BCG_att6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6T"]
, na.rm = TRUE)
, nt_BCG_attNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(BCG_ATTR)]
, na.rm = TRUE)
### BCG, pi ----
, pi_BCG_att12 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att123 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1234 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG2_att1234b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1236 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1236sp = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE) / sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6"
| BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE)
, pi_BCG_att1236b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att12346b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i236i = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att2 = 100 * sum(N_TAXA[BCG_ATTR == "2"]
, na.rm = TRUE) / ni_total
, pi_BCG_att2native = 100 * sum(N_TAXA[BCG_ATTR == "2"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att23_scc = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3")
& SCC == TRUE]
, na.rm = TRUE) / ni_total
, pi_BCG_att3 = 100 * sum(N_TAXA[BCG_ATTR == "3"]
, na.rm = TRUE) / ni_total
, pi_BCG_att3native = 100 * sum(N_TAXA[BCG_ATTR == "3"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4 = 100 * sum(N_TAXA[BCG_ATTR == "4"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4native = 100 * sum(N_TAXA[BCG_ATTR == "4"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4b = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4m = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w5 = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE)) / ni_total
, pi_BCG_att5 = 100 * sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE) / ni_total
, pi_BCG_att5native = 100 * sum(N_TAXA[BCG_ATTR == "5"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att55a6a = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56a = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5a6a = 100 * sum(N_TAXA[(BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56t = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6 = 100 * sum(N_TAXA[BCG_ATTR == "6"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6i = 100 * sum(N_TAXA[BCG_ATTR == "6I"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6m = 100 * sum(N_TAXA[BCG_ATTR == "6M"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6t = 100 * sum(N_TAXA[BCG_ATTR == "6T"]
, na.rm = TRUE) / ni_total
, pi_BCG_att66a = 100 * sum(N_TAXA[(BCG_ATTR == "6"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att66a6b = 100 * sum(N_TAXA[(BCG_ATTR == "6"
| BCG_ATTR == "6A"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att66s6t = 100 * sum(N_TAXA[BCG_ATTR == "6"
| BCG_ATTR == "6S"
| BCG_ATTR == "6T"]
, na.rm = TRUE) / ni_total
, pi_BCG_attNA = 100 * sum(N_TAXA[is.na(BCG_ATTR)]
, na.rm = TRUE) / ni_total
### BCG, pt----
, pt_BCG_att12 = 100 * nt_BCG_att12 / nt_total
, pt_BCG_att123 = 100 * nt_BCG_att123 / nt_total
, pt_BCG2_att123b = 100 * nt_BCG2_att123b / nt_total
, pt_BCG_att1234 = 100 * nt_BCG_att1234 / nt_total
, pt_BCG2_att1234b = 100 * nt_BCG2_att1234b / nt_total
, pt_BCG_att1236 = 100 * nt_BCG_att1236 / nt_total
, pt_BCG_att1236b = 100 * nt_BCG_att1236b / nt_total
, pt_BCG_att1236sp = 100 * nt_BCG_att1236 / (nt_BCG_att1236 +
nt_BCG_att55a6a)
, pt_BCG_att12346b = 100 * nt_BCG_att12346b / nt_total
, pt_BCG_att1i236i = 100 * nt_BCG_att1i236i / nt_total
, pt_BCG_att2 = 100 * nt_BCG_att2 / nt_total
, pt_BCG_att2native = 100 * nt_BCG_att2native / nt_total
, pt_BCG_att23_scc = 100 * nt_BCG_att23_scc / nt_total
, pt_BCG_att3 = 100 * nt_BCG_att3 / nt_total
, pt_BCG_att3native = 100 * nt_BCG_att3native / nt_total
, pt_BCG_att4 = 100 * nt_BCG_att4 / nt_total
, pt_BCG_att4native = 100 * nt_BCG_att4native / nt_total
, pt_BCG_att4b = 100 * nt_BCG_att4b / nt_total
, pt_BCG_att4m = 100 * nt_BCG_att4m / nt_total
, pt_BCG_att4w = 100 * nt_BCG_att4w / nt_total
, pt_BCG_att4w5 = 100 * nt_BCG_att4w5 / nt_total
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
, pt_BCG_att5native = 100 * nt_BCG_att5native / nt_total
, pt_BCG_att55a6a = 100 * nt_BCG_att55a6 / nt_total
, pt_BCG_att56t = 100 * nt_BCG_att56t / nt_total
, pt_BCG_att6i = 100 * nt_BCG_att6i / nt_total
, pt_BCG_att6m = 100 * nt_BCG_att6m / nt_total
, pt_BCG_att6t = 100 * nt_BCG_att6t / nt_total
, pt_BCG_attNA = 100 * nt_BCG_attNA / nt_total
### BCG, pi_dom----
, pi_dom01_BCG_att4 = 100 * max(0
, N_TAXA[(BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att45 = 100 * max(0
, N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5 = 100 * max(0
, N_TAXA[(BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5a = 100 * max(0
, N_TAXA[(BCG_ATTR == "5A")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5a6a = 100 * max(0
, N_TAXA[(BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att566a = 100 * max(0, N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
## Thermal Indicators ####
## nt_ti
, nt_ti_corecold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_CORECOLD == TRUE]
, na.rm = TRUE)
, nt_ti_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COLD == TRUE]
, na.rm = TRUE)
, nt_ti_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COOL == TRUE]
, na.rm = TRUE)
, nt_ti_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_WARM == TRUE]
, na.rm = TRUE)
, nt_ti_eury = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_EURY == TRUE]
, na.rm = TRUE)
, nt_ti_na = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_NA == TRUE]
, na.rm = TRUE)
, nt_ti_corecold_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_CORECOLD == TRUE
| TI_COLD == TRUE)]
, na.rm = TRUE)
, nt_ti_cool_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_COOL == TRUE
| TI_WARM == TRUE)]
, na.rm = TRUE)
## pi_ti
, pi_ti_corecold = 100 * sum(N_TAXA[TI_CORECOLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cold = 100 * sum(N_TAXA[TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool = 100 * sum(N_TAXA[TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm = 100 * sum(N_TAXA[TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_eury = 100 * sum(N_TAXA[TI_EURY == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_na = 100 * sum(N_TAXA[TI_NA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_corecold_cold = 100 * sum(N_TAXA[TI_CORECOLD == TRUE |
TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool_warm = 100 * sum(N_TAXA[TI_COOL == TRUE |
TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
## pt_ti
, pt_ti_corecold = 100 * nt_ti_corecold / nt_total
, pt_ti_cold = 100 * nt_ti_cold / nt_total
, pt_ti_cool = 100 * nt_ti_cool / nt_total
, pt_ti_warm = 100 * nt_ti_warm / nt_total
, pt_ti_eury = 100 * nt_ti_eury / nt_total
, pt_ti_na = 100 * nt_ti_na / nt_total
, pt_ti_corecold_cold = 100 * nt_ti_corecold_cold / nt_total
, pt_ti_cool_warm = 100 * nt_ti_cool_warm / nt_total
## Elevation ----
, nt_elev_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ELEVATION_LOW == TRUE]
, na.rm = TRUE)
, nt_elev_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ELEVATION_HIGH == TRUE]
, na.rm = TRUE)
## Gradient ----
, nt_grad_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_LOW == TRUE]
, na.rm = TRUE)
, nt_grad_mod = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_MOD == TRUE]
, na.rm = TRUE)
, nt_grad_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_HIGH == TRUE]
, na.rm = TRUE)
## WS_Area ----
, nt_wsarea_small = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_S == TRUE]
, na.rm = TRUE)
, nt_wsarea_medium = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_M == TRUE]
, na.rm = TRUE)
, nt_wsarea_large = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_L == TRUE]
, na.rm = TRUE)
, nt_wsarea_xlarge = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_XL == TRUE]
, na.rm = TRUE)
## Reproduction ----
### Repro, nt ----
, nt_repro_broadcaster = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_BCAST == TRUE]
, na.rm = TRUE)
, nt_repro_nestsimp = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_NS == TRUE]
, na.rm = TRUE)
, nt_repro_nestcomp = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_NC == TRUE]
, na.rm = TRUE)
, nt_repro_bearer = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_BEAR == TRUE]
, na.rm = TRUE)
, nt_repro_migratory = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_MIG == TRUE]
, na.rm = TRUE)
, nt_repro_lithophil = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_LITH == TRUE]
, na.rm = TRUE)
### Repro, pi ----
, pi_repro_broadcaster = 100 * sum(N_TAXA[REPRO_BCAST == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_nestsimp = 100 * sum(N_TAXA[REPRO_NS == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_nestcomp = 100 * sum(N_TAXA[REPRO_NC == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_bearer = 100 * sum(N_TAXA[REPRO_BEAR == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_migratory = 100 * sum(N_TAXA[REPRO_MIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_lithophil = 100 * sum(N_TAXA[REPRO_LITH == TRUE]
, na.rm = TRUE) / ni_total
### Repro, pt ----
, pt_repro_broadcaster = 100 * nt_repro_broadcaster / nt_total
, pt_repro_nestsimp = 100 * nt_repro_nestsimp / nt_total
, pt_repro_nestcomp = 100 * nt_repro_nestcomp / nt_total
, pt_repro_bearer = 100 * nt_repro_bearer / nt_total
, pt_repro_migratory = 100 * nt_repro_migratory / nt_total
, pt_repro_lithophil = 100 * nt_repro_lithophil / nt_total
## Habitat ####
# BCG Great Plains 2021
# W = water column
# B = benthic
# F = fluvial
#
# nt_habitat
, nt_habitat_b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_B == TRUE]
, na.rm = TRUE)
, nt_habitat_w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_W == TRUE]
, na.rm = TRUE)
, nt_habitat_f = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_F == TRUE]
, na.rm = TRUE)
## pi_habitat
, pi_habitat_b = 100 * sum(N_TAXA[HABITAT_B == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_w = 100 * sum(N_TAXA[HABITAT_W == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_f = 100 * sum(N_TAXA[HABITAT_F == TRUE]
, na.rm = TRUE) / ni_total
## pt_habitat
, pt_habitat_b = 100 * nt_habitat_b / nt_total
, pt_habitat_w = 100 * nt_habitat_w / nt_total
, pt_habitat_f = 100 * nt_habitat_f / nt_total
## SPECIAL ----
# odd ball metrics that don't fit the above groupings
# OR are really different and probably only applicable
# to a specific entity
#### New Mexico Fish BCG
, nt_piscivore_BCG_att66s6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PI == TRUE
& (BCG_ATTR == "6"
| BCG_ATTR == "6S"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_LLNLB = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE == "LLNLB"]
, na.rm = TRUE)
, nt_Cyprin_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CYPRINIDAE"
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, ni_Hybognathus_amarus = sum(N_TAXA[TAXAID == "HYBOGNATHUS AMARUS"]
, na.rm = TRUE)
, x_TrophicCats = dplyr::n_distinct(TROPHIC, na.rm = TRUE)
### Great Plains BCG, 2024-04-25
, x_BCG_Mean = mean(TOLVAL2, na.rm = TRUE)
, nt_PupKilli = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TAXAID == "CYPRINODON RUBROFLUVIATILIS" #RED RIVER PUPFISH
| TAXAID == "FUNDULUS KANSAE" #NORTHERN PLAINS KILLIFISH
| TAXAID == "FUNDULUS ZEBRINUS")] #PLAINS KILLIFISH
, na.rm = TRUE)
# Great Plains 2024-08-06
#### GP, SALT
, pi_salt = 100 * sum(N_TAXA[TYPE_SALT == TRUE]
, na.rm = TRUE) / ni_total
#### GP, NPL
, pi_NPL = 100 * sum(N_TAXA[TYPE_NPL == TRUE]
, na.rm = TRUE) / ni_total
### Minnesota (Red Lakes) FIBI, 2024-06-01----
#### MN, nt
, nt_total_ExclSchool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0
& TYPE_SCHOOL != TRUE]
, na.rm = TRUE)
#### MN, ni
, ni_total_ExclSchool = sum(N_TAXA[TYPE_SCHOOL != TRUE]
, na.rm = TRUE)
, ni_total_notoler_mn = sum(N_TAXA[TOLER_T != TRUE]
, na.rm = TRUE)
#### MN, nt, HABITAT
, nt_coldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_CW == TRUE]
, na.rm = TRUE)
, nt_natcoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_CWN == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_hw_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_HW_noT == TRUE]
, na.rm = TRUE)
, nt_wetland_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_WE_noT == TRUE]
, na.rm = TRUE)
#### MN, nt, REPRO
, nt_serialspawner = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& REPRO_SER == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_simplelithophil = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& REPRO_SILI == TRUE]
, na.rm = TRUE)
#### MN, nt, TOLER
, nt_tv_sens = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_S == TRUE]
, na.rm = TRUE)
, nt_tv_senscoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_SCW == TRUE]
, na.rm = TRUE)
, nt_tv_tolercoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_TCW == TRUE]
, na.rm = TRUE)
, nt_tv_toler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_T == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_tv_vtoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_VT == TRUE]
, na.rm = TRUE)
#### MN, nt, TROPHIC
, nt_beninsct_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_BI_noT == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_detritivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_DE == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_gen = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_GE == TRUE]
, na.rm = TRUE)
, nt_insectivore_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IN_noT == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_omnivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_OM == TRUE]
, na.rm = TRUE) # MN, nt for pt
#### MN, nt, TYPE
, nt_dartersculpin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_DS == TRUE]
, na.rm = TRUE)
, nt_darterscultpinsucker = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_DSS == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_pioneer = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_PI == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_shortlived = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_SL == TRUE]
, na.rm = TRUE)
### MN, pi, HABITAT
, pi_hw_notoler_ExclSchool = 100 * sum(N_TAXA[HABITAT_HW_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_wetland_notoler_ExclSchool = 100 * sum(N_TAXA[HABITAT_WE_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_natcoldwater_ExclSchool = 100 * sum(N_TAXA[HABITAT_CWN == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, REPRO
, pi_ma2_ExclShool = 100 * sum(N_TAXA[REPRO_MA2 == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_ma3_notoler_ExclSchool = 100 * sum(N_TAXA[REPRO_MA3_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_nonlithophil_ExclSchool = 100 * sum(N_TAXA[REPRO_NE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_serialspawner_ExclSchool = 100 * sum(N_TAXA[REPRO_SER == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_simplelithophil_ExclSchool = 100 * sum(N_TAXA[REPRO_SILI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TROPHIC
, pi_detritivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_DE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_gen_ExclSchool = 100 * sum(N_TAXA[TROPHIC_GE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_herbivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_HB == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_insctCypr_ExclSchool = 100 * sum(N_TAXA[TROPHIC_IN_CYP == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
# , ni_insectivore_notoler_ExclSchool = sum(N_TAXA[TROPHIC_IN_noT == TRUE
# & TYPE_SCHOOL == FALSE]
# , na.rm = TRUE)
, pi_insectivore_notoler_ExclSchool = 100 * sum(N_TAXA[TROPHIC_IN_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_piscivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_PI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TOLER
, pi_tv_intol_ExclSchool = 100 * sum(N_TAXA[TOLER_I == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_intolcoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_ICW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_sens_ExclSchool = 100 * sum(N_TAXA[TOLER_S == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_senscoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_SCW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_toler_ExclSchool = 100 * sum(N_TAXA[TOLER_T == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_tolercoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_TCW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TYPE
, pi_exotic_ExclSchool = 100 * sum(N_TAXA[TYPE_EX == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_minnow_notoler_ExclSchool = 100 * sum(N_TAXA[TYPE_MIN_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_Perciformes_ExclSchool = 100 * sum(N_TAXA[TYPE_PERC == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_pioneer_ExclShool = 100 * sum(N_TAXA[TYPE_PI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_shortlived_ExclSchool = 100 * sum(N_TAXA[TYPE_SL == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, other
, pi_dom02_ExclSchool = 100 * max(ni_dom02_ExclSchool, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pt, HABITAT
, pt_natcoldwater = 100 * nt_natcoldwater / nt_total
#### MN, pt, REPRO
, pt_serialspawner = 100 * nt_serialspawner / nt_total
, pt_simplelithophil = 100 * nt_simplelithophil / nt_total
#### MN, pt, TOLER
, pt_tv_sens = 100 * nt_tv_sens / nt_total
, pt_tv_senscoldwater = 100 * nt_tv_senscoldwater / nt_total
, pt_tv_toler = 100 * nt_tv_toler / nt_total
, pt_tv_vtoler = 100 * nt_tv_vtoler / nt_total
#### MN, pt, TROPHIC
, pt_beninsct_notoler = 100 * nt_beninsct_notoler / nt_total
, pt_detritivore = 100 * nt_detritivore / nt_total
, pt_gen = 100 * nt_gen / nt_total
, pt_insectivore_notoler = 100 * nt_insectivore_notoler / nt_total
, pt_omnivore = 100 * nt_omnivore / nt_total
#### MN, pt, TYPE
, pt_darterscultpinsucker = 100 * nt_darterscultpinsucker / nt_total
, pt_pioneer = 100 * nt_pioneer / nt_total
#### MN, x
, ni_m_notoler = ni_total_notoler_mn / length_m
#### MN, DELT
, pi_delt_ExclSchool = 100 * sum(N_ANOMALIES[TYPE_SCHOOL != TRUE]
, na.rm = TRUE) / ni_total_ExclSchool
#
# name changes ####
# # MBSS metric names
# , STRMAREA = area
# , TOTCNT = ni_total
# , ABUNSQM = ni_m2
# , PABDOM = pi_dom01
# , TOTBIOM = x_biomass_total
# , BIOM_MSQ = x_biomass_m2
# , NUMBENTSP = nt_benthic
# # , NUMBROOK = ni_brooktrout
# , PBROOK = pi_brooktrout
# # , NUMGEOMIV = ni_genomninvrt
# , PGEOMIV = pi_genomninvrt
# # , NUMIS = ni_insectivore
# , P_IS = pi_insectivore
# # , NUMLITH = ni_lithophil
# , P_LITH = pi_lithophil
# # , NUMROUND = ni_rbs
# , PROUND = pi_rbs
# # , NUMSCULP = ni_sculpin
# , PSCULP = pi_sculpin
# # , NUMTOL = ni_tv_toler
# , PTOL = pi_tv_toler
#
)## met.val.END
if (verbose == TRUE) {
# 7
debug_topic <- "clean up"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
#
# replace NA with 0
met.val[is.na(met.val)] <- 0
#
# # # subset to only metrics specified by user
# # if (!is.null(MetricNames)) {
# # met.val <- met.val[,c(Index_Name, SITE, INDEX_CLASS, ACREAGE, LEN_SAMP, MetricNames)]
# # }
# myFlds_Remove <- c("ni_total", "pi_rbs",
# , "pi_brooktrout", "pi_sculpin", "nt_total"
# , "nt_benthic", "pi_lithophil",
# , "pi_genomninvrt", "pi_insectivore",
# , "pi_tv_toler", "pi_dom01", "area", "ni_m2"
# , "x_biomass_total", "x_biomass_m2")
# met.val <- met.val[,-match(myFlds_Remove,names(met.val))]
# # subset to only metrics specified by user
if (verbose == TRUE) {
# 8
debug_topic <- "subset"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(MetricNames)) {
#met.val <- met.val
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (verbose == TRUE) {
# 9
debug_topic <- "extra fields"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>%
dplyr::group_by(.dots = c("SAMPLEID", cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val)
, by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# adjust ----
# #
# # Adjust metrics (MBSS always adjust so remove IF/THEN)
# # added as extra columns to output
# #if (boo.Adjust==TRUE) {##IF.boo.Ajust.START
# # MBSS.2005.Fish
# # nt_benthic
# met.val[,"NUMBENTSP_Obs"] <- met.val[,"NUMBENTSP"]
# # Expected constants
# ## m
# met.val[,"NUMBENTSP_m"] <- NA
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="COASTAL"] <- 1.69
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="EPIEDMONT"] <- 1.25
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="HIGHLAND"] <- 1.23
# ## b
# met.val[,"NUMBENTSP_b"] <- NA
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="COASTAL"] <- -3.33
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="EPIEDMONT"] <- -2.36
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="HIGHLAND"] <- -2.35
# # Calc Expected
# met.val[,"NUMBENTSP_Exp"] <- (met.val[,"NUMBENTSP_m"] * log10(met.val[,"ACREAGE"])) + met.val[,"NUMBENTSP_b"]
# # Calc Adjusted
# met.val[,"NUMBENTSP_Adj"] <- met.val[,"NUMBENTSP_Obs"] / met.val[,"NUMBENTSP_Exp"]
# # Rename base metric with adjusted value
# met.val[,"NUMBENTSP"] <- met.val[,"NUMBENTSP_Adj"]
# # NA to zero
# met.val[,"NUMBENTSP"][is.na(met.val[,"NUMBENTSP"])] <- 0
#
# #}##IF.boo.Ajust.END
#
# df to report back
if (verbose == TRUE) {
# 10
debug_topic <- "return results"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
return(df.return)
}##FUNCTION.metric.values.fish.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Algae
#'
#' @description Subfunction of metric.values for use with Algae.
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.algae <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.Shiny = FALSE
, verbose) {
time_start <- Sys.time()
# global variable bindings ----
N_TAXA <- NULL
NONTARGET <- SAMPLEID <- INDEX_NAME <- INDEX_CLASS <- ni_total <- TAXAID <-
EXCLUDE <- GENUS <- LOW_N <- HIGH_N <- LOW_P <- HIGH_P <- BC_1 <- BC_2 <-
BC_3 <- BC_4 <- BC_5 <- PT_1 <- PT_2 <- PT_3 <- PT_4 <- PT_5 <-
SALINITY_1 <- SALINITY_2 <- SALINITY_3 <- SALINITY_4 <- O_1 <- O_2 <- O_3 <-
O_4 <- O_5 <- SESTONIC_HABIT <- BENTHIC_HABIT <- BAHLS_1 <- BAHLS_2 <-
BAHLS_3 <- TROPHIC_1 <- TROPHIC_2 <- TROPHIC_3 <- TROPHIC_4 <- TROPHIC_5 <-
TROPHIC_6 <- TROPHIC_7 <- SAP_1 <- SAP_2 <- SAP_3 <- SAP_4 <- SAP_5 <-
NON_N_FIXER <- N_FIXER <- HIGHLY_MOTILE <- MODERATELY_MOTILE <-
NON_MOTILE <- SLIGHTLY_MOTILE <- WEAKLY_MOTILE <- BIG <- SMALL <- MEDIUM <-
VERY_BIG <- VERY_SMALL <- ADNATE <- STALKED <- HIGHLY_MOTILE.1 <- ARAPHID <-
DIAT_CL <- BEN_SES <- DIAT_CA <- DIAT_COND <- DIATAS_TN <- DIATAS_TP <-
MOTILITY <- NF <- pi_DIAT_CL_1 <- nt_Achnan_Navic <- nt_total <-
nt_HIGH_N <- nt_LOW_N <- nt_HIGH_P <- nt_LOW_P <- nt_BC_1 <- nt_BC_2 <-
nt_BC_3 <- nt_BC_4 <- nt_BC_5 <- nt_BC_12 <- nt_BC_45 <- nt_PT_1 <-
nt_PT_2 <- nt_PT_3 <- nt_PT_4 <- nt_PT_5 <- nt_PT_12 <- nt_SALINITY_1 <-
nt_SALINITY_2 <- nt_SALINITY_3 <- nt_SALINITY_4 <- nt_SALINITY_34 <-
nt_O_1 <- nt_O_2 <- nt_O_3 <- nt_O_4 <- nt_O_5 <- nt_O_345 <-
nt_SESTONIC_HABIT <- nt_BENTHIC_HABIT <- nt_BAHLS_1 <- nt_BAHLS_2 <-
nt_BAHLS_3 <- nt_TROPHIC_1 <- nt_TROPHIC_2 <- nt_TROPHIC_3 <-
nt_TROPHIC_4 <- nt_TROPHIC_5 <- nt_TROPHIC_6 <- nt_TROPHIC_7 <-
nt_TROPHIC_456 <- nt_SAP_1 <- nt_SAP_2 <- nt_SAP_3 <- nt_SAP_4 <-
nt_SAP_5 <- nt_NON_N_FIXER <- nt_N_FIXER <- nt_HIGHLY_MOTILE <-
nt_MODERATELY_MOTILE <- nt_NON_MOTILE <- nt_SLIGHTLY_MOTILE <-
nt_WEAKLY_MOTILE <- nt_BIG <- nt_SMALL <- nt_MEDIUM <- nt_VERY_BIG <-
nt_VERY_SMALL <- nt_ADNATE <- nt_STALKED <- nt_HIGHLY_MOTILE.1 <-
nt_ARAPHID <- nt_DIAT_CL_1 <- nt_DIAT_CL_2 <- nt_BEN_SES_1 <-
nt_BEN_SES_2 <- nt_DIAT_CA_1 <- nt_DIAT_CA_2 <- nt_DIAT_COND_1 <-
nt_DIAT_COND_2 <- nt_DIATAS_TN_1 <- nt_DIATAS_TN_2 <- nt_DIATAS_TP_1 <-
nt_DIATAS_TP_2 <- nt_MOTILITY_1 <- nt_MOTILITY_2 <- nt_NF_1 <- nt_NF_2 <-
TOLVAL <- REF_INDICATORS <- nt_Sens_810 <- nt_RefIndicators <- nt_Tol_13 <-
POLL_TOL <- NULL
nt_TROPHIC_12 <- nt_TROPHIC_56 <- pi_BC_12 <- pt_TROPHIC_12 <-
pt_TROPHIC_56 <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC----
# QC, Required Fields
## QC, Missing Cols ----
# col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
# , "PHYLUM", "ORDER", "FAMILY", "GENUS"
# )
# col.req_logical <- c("EXCLUDE", "NONTARGET")
# col.req_numeric <- c("N_TAXA")
# col.req <- c(col.req_character, col.req_logical, col.req_numeric)
col.req <- c("INDEX_NAME", "INDEX_CLASS", "SAMPLEID","TAXAID","N_TAXA"
,"EXCLUDE","NONTARGET"
,"PHYLUM","ORDER","FAMILY","GENUS","BC_USGS"
,"TROPHIC_USGS","SAP_USGS","PT_USGS","O_USGS","SALINITY_USGS"
,"BAHLS_USGS","P_USGS","N_USGS","HABITAT_USGS","N_FIXER_USGS"
,"MOTILITY_USGS","SIZE_USGS","HABIT_USGS","MOTILE2_USGS"
,"TOLVAL","DIATOM_ISA","DIAT_CL","POLL_TOL","BEN_SES"
,"DIATAS_TP","DIATAS_TN","DIAT_COND","DIAT_CA","MOTILITY"
,"NF")
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {##IF.num.col.req.missing.START
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" ", myPrompt.01, myPrompt.02, " ", myPrompt.03, myPrompt.04
, myPrompt.05, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
# special condition for Shiny
#Shiny counts as interactive()==TRUE but cannot access this prompt in Shiny.
if (boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
myDF[,col.req.missing] <- NA
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude ----
# as TRUE/FALSE
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {##IF.Exclude.T.START
warning("EXCLUDE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, NonTarget ----
# as TRUE/FALSE
NonTarget.F <- sum(myDF$NONTARGET == FALSE, na.rm = TRUE)
if (NonTarget.F == 0) {##IF.Exclude.T.START
warning("NONTARGET column does not have any FALSE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, TolVal----
# need as numeric, if have "NA" as character it fails
TolVal_Char_NA <- myDF[, "TOLVAL"] == "NA"
if (sum(TolVal_Char_NA, na.rm = TRUE) > 0) {
myDF[TolVal_Char_NA, "TOLVAL"] <- NA
myDF[, "TOLVAL"] <- as.numeric(myDF[, "TOLVAL"])
}##IF ~ TOLVAL ~ END
# Data Munging----
# Remove NonTarget Taxa (added back 20200715, missing since 20200224)
# Function fails if all NA (e.g., column was missing) (20200724)
myDF <- myDF %>% dplyr::filter(NONTARGET != TRUE | is.na(NONTARGET))
# Convert values to upper case (FFG, Habit, Life_Cycle)
myDF[, "BC_USGS"] <- toupper(myDF[, "BC_USGS"])
myDF[, "PT_USGS"] <- toupper(myDF[, "PT_USGS"])
myDF[, "O_USGS"] <- toupper(myDF[, "O_USGS"])
myDF[, "SALINITY_USGS"] <- toupper(myDF[, "SALINITY_USGS"])
myDF[, "P_USGS"] <- toupper(myDF[, "P_USGS"])
myDF[, "N_USGS"] <- toupper(myDF[, "N_USGS"])
myDF[, "HABITAT_USGS"] <- toupper(myDF[, "HABITAT_USGS"])
myDF[, "BAHLS_USGS"] <- toupper(myDF[, "BAHLS_USGS"])
myDF[, "TROPHIC_USGS"] <- toupper(myDF[, "TROPHIC_USGS"])
myDF[, "DIATOM_ISA"] <- toupper(myDF[, "DIATOM_ISA"])
myDF[, "SAP_USGS"] <- toupper(myDF[, "SAP_USGS"])
myDF[, "N_FIXER_USGS"] <- toupper(myDF[, "N_FIXER_USGS"])
myDF[, "MOTILITY_USGS"] <- toupper(myDF[, "MOTILITY_USGS"])
myDF[, "SIZE_USGS"] <- toupper(myDF[, "SIZE_USGS"])
myDF[, "HABIT_USGS"] <- toupper(myDF[, "HABIT_USGS"])
myDF[, "MOTILE2_USGS"] <- toupper(myDF[, "MOTILE2_USGS"])
myDF[, "DIATOM_ISA"] <- toupper(myDF[, "DIATOM_ISA"])
# Add extra columns for some fields
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "CN, CB" is both "CN" and "CB"
myDF[, "BC_1"] <- grepl("BC_1", myDF[, "BC_USGS"])
myDF[, "BC_2"] <- grepl("BC_2", myDF[, "BC_USGS"])
myDF[, "BC_3"] <- grepl("BC_3", myDF[, "BC_USGS"])
myDF[, "BC_4"] <- grepl("BC_4", myDF[, "BC_USGS"])
myDF[, "BC_5"] <- grepl("BC_5", myDF[, "BC_USGS"])
myDF[, "PT_1"] <- grepl("PT_1", myDF[, "PT_USGS"])
myDF[, "PT_2"] <- grepl("PT_2", myDF[, "PT_USGS"])
myDF[, "PT_3"] <- grepl("PT_3", myDF[, "PT_USGS"])
myDF[, "PT_4"] <- grepl("PT_4", myDF[, "PT_USGS"])
myDF[, "PT_5"] <- grepl("PT_5", myDF[, "PT_USGS"])
myDF[, "O_1"] <- grepl("O_1", myDF[, "O_USGS"])
myDF[, "O_2"] <- grepl("O_2", myDF[, "O_USGS"])
myDF[, "O_3"] <- grepl("O_3", myDF[, "O_USGS"])
myDF[, "O_4"] <- grepl("O_4", myDF[, "O_USGS"])
myDF[, "O_5"] <- grepl("O_5", myDF[, "O_USGS"])
myDF[, "SALINITY_1"] <- grepl("SALINITY_1", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_2"] <- grepl("SALINITY_2", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_3"] <- grepl("SALINITY_3", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_4"] <- grepl("SALINITY_4", myDF[, "SALINITY_USGS"])
myDF[, "HIGH_P"] <- grepl("HIGH_P", myDF[, "P_USGS"])
myDF[, "LOW_P"] <- grepl("LOW_P", myDF[, "P_USGS"])
myDF[, "HIGH_N"] <- grepl("HIGH_N", myDF[, "N_USGS"])
myDF[, "LOW_N"] <- grepl("LOW_N", myDF[, "N_USGS"])
myDF[, "BENTHIC_HABIT"] <- grepl("BENTHIC_HABIT", myDF[, "HABITAT_USGS"])
myDF[, "SESTONIC_HABIT"] <- grepl("SESTONIC_HABIT", myDF[, "HABITAT_USGS"])
myDF[, "BAHLS_1"] <- grepl("BAHLS_1", myDF[, "BAHLS_USGS"])
myDF[, "BAHLS_2"] <- grepl("BAHLS_2", myDF[, "BAHLS_USGS"])
myDF[, "BAHLS_3"] <- grepl("BAHLS_3", myDF[, "BAHLS_USGS"])
myDF[, "TROPHIC_1"] <- grepl("TROPHIC_1", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_2"] <- grepl("TROPHIC_2", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_3"] <- grepl("TROPHIC_3", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_4"] <- grepl("TROPHIC_4", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_5"] <- grepl("TROPHIC_5", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_6"] <- grepl("TROPHIC_6", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_7"] <- grepl("TROPHIC_7", myDF[, "TROPHIC_USGS"])
myDF[, "SAP_1"] <- grepl("SAP_1", myDF[, "SAP_USGS"])
myDF[, "SAP_2"] <- grepl("SAP_2", myDF[, "SAP_USGS"])
myDF[, "SAP_3"] <- grepl("SAP_3", myDF[, "SAP_USGS"])
myDF[, "SAP_4"] <- grepl("SAP_4", myDF[, "SAP_USGS"])
myDF[, "SAP_5"] <- grepl("SAP_5", myDF[, "SAP_USGS"])
myDF[, "NON_N_FIXER"] <- grepl("NON_N_FIXER", myDF[, "N_FIXER_USGS"])
myDF[, "N_FIXER"] <- grepl("\\bN_FIXER\\b", myDF[, "N_FIXER_USGS"])
myDF[, "HIGHLY_MOTILE"] <- grepl("HIGHLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "MODERATELY_MOTILE"] <- grepl("MODERATELY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "NON_MOTILE"] <- grepl("NON_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "SLIGHTLY_MOTILE"] <- grepl("SLIGHTLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "WEAKLY_MOTILE"] <- grepl("WEAKLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "BIG"] <- grepl("\\bBIG\\b", myDF[, "SIZE_USGS"])
myDF[, "MEDIUM"] <- grepl("MEDIUM", myDF[, "SIZE_USGS"])
myDF[, "SMALL"] <- grepl("\\bSMALL\\b", myDF[, "SIZE_USGS"])
myDF[, "VERY_BIG"] <- grepl("VERY_BIG", myDF[, "SIZE_USGS"])
myDF[, "VERY_SMALL"] <- grepl("VERY_SMALL", myDF[, "SIZE_USGS"])
myDF[, "ADNATE"] <- grepl("ADNATE", myDF[, "HABIT_USGS"])
myDF[, "STALKED"] <- grepl("STALKED", myDF[, "HABIT_USGS"])
myDF[, "HIGHLY_MOTILE.1"] <- grepl("HIGHLY_MOTILE.1", myDF[, "MOTILE2_USGS"])
myDF[, "ARAPHID"] <- grepl("ARAPHID", myDF[, "MOTILE2_USGS"])
myDF[, "REF_INDICATORS"] <- grepl("^REF", myDF[, "DIATOM_ISA"])
# Metric Calc----
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF, SAMPLEID, INDEX_NAME
, INDEX_CLASS)
#
## Individuals ----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, li_total = log(ni_total)
## Number of Taxa ----
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0]
, na.rm = TRUE)
### Phylo----
, nt_Achnan_Navic = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (GENUS == "Achnanthidium"
| GENUS == "Navicula")]
, na.rm = TRUE)
### N_USGS----
, nt_LOW_N = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LOW_N == TRUE]
, na.rm = TRUE)
, nt_HIGH_N = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGH_N == TRUE]
, na.rm = TRUE)
### P_USGS----
, nt_LOW_P = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LOW_P == TRUE]
, na.rm = TRUE)
, nt_HIGH_P = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGH_P == TRUE]
, na.rm = TRUE)
### BC_USGS----
, nt_BC_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_1 == TRUE]
, na.rm = TRUE)
, nt_BC_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_2 == TRUE]
, na.rm = TRUE)
, nt_BC_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_3 == TRUE]
, na.rm = TRUE)
, nt_BC_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_4 == TRUE]
, na.rm = TRUE)
, nt_BC_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_5 == TRUE]
, na.rm = TRUE)
, nt_BC_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BC_1 == TRUE
| BC_2 == TRUE)]
, na.rm = TRUE)
, nt_BC_45 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BC_4 == TRUE
| BC_5 == TRUE)]
, na.rm = TRUE)
### PT_USGS----
, nt_PT_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_1 == TRUE]
, na.rm = TRUE)
, nt_PT_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_2 == TRUE]
, na.rm = TRUE)
, nt_PT_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_3 == TRUE]
, na.rm = TRUE)
, nt_PT_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_4 == TRUE]
, na.rm = TRUE)
, nt_PT_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_5 == TRUE]
, na.rm = TRUE)
, nt_PT_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (PT_1 == TRUE
| PT_2 == TRUE)]
, na.rm = TRUE)
### SALINITY_USGS----
, nt_SALINITY_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_1 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_2 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_3 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_4 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (SALINITY_1 == TRUE
| SALINITY_2 == TRUE)]
, na.rm = TRUE)
, nt_SALINITY_34 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (SALINITY_3 == TRUE
| SALINITY_4 == TRUE)]
, na.rm = TRUE)
### O_USGS----
, nt_O_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_1 == TRUE]
, na.rm = TRUE)
, nt_O_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_2 == TRUE]
, na.rm = TRUE)
, nt_O_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_3 == TRUE]
, na.rm = TRUE)
, nt_O_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_4 == TRUE]
, na.rm = TRUE)
, nt_O_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_5 == TRUE]
, na.rm = TRUE)
, nt_O_345 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (O_3 == TRUE
| O_4 == TRUE
| O_5 == TRUE)]
, na.rm = TRUE)
### HABITAT_USGS----
, nt_SESTONIC_HABIT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SESTONIC_HABIT == TRUE]
, na.rm = TRUE)
, nt_BENTHIC_HABIT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BENTHIC_HABIT == TRUE]
, na.rm = TRUE)
### BAHLS_USGS----
, nt_BAHLS_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_1 == TRUE)]
, na.rm = TRUE)
, nt_BAHLS_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_2 == TRUE)]
, na.rm = TRUE)
, nt_BAHLS_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_3 == TRUE)]
, na.rm = TRUE)
### TROPHIC_USGS----
, nt_TROPHIC_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_1 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_2 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_3 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_4 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_5 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_6 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_7 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_7 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_1 == TRUE
| TROPHIC_2 == TRUE)]
, na.rm = TRUE)
, nt_TROPHIC_456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_4 == TRUE
| TROPHIC_5 == TRUE
| TROPHIC_6 == TRUE)]
, na.rm = TRUE)
, nt_TROPHIC_56 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_5 == TRUE
| TROPHIC_6 == TRUE)]
, na.rm = TRUE)
### SAP_USGS----
, nt_SAP_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_1 == TRUE]
, na.rm = TRUE)
, nt_SAP_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_2 == TRUE]
, na.rm = TRUE)
, nt_SAP_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_3 == TRUE]
, na.rm = TRUE)
, nt_SAP_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_4 == TRUE]
, na.rm = TRUE)
, nt_SAP_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_5 == TRUE]
, na.rm = TRUE)
### N_FIXER_USGS----
, nt_NON_N_FIXER = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NON_N_FIXER == TRUE]
, na.rm = TRUE)
, nt_N_FIXER = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_FIXER == TRUE]
, na.rm = TRUE)
### MOTILITY_USGS----
, nt_HIGHLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGHLY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_MODERATELY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MODERATELY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_NON_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NON_MOTILE == TRUE]
, na.rm = TRUE)
, nt_SLIGHTLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SLIGHTLY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_WEAKLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WEAKLY_MOTILE == TRUE]
, na.rm = TRUE)
### SIZE_USGS----
, nt_BIG = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BIG == TRUE]
, na.rm = TRUE)
, nt_SMALL = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SMALL == TRUE]
, na.rm = TRUE)
, nt_MEDIUM = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MEDIUM == TRUE]
, na.rm = TRUE)
, nt_VERY_BIG = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& VERY_BIG == TRUE]
, na.rm = TRUE)
, nt_VERY_SMALL = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& VERY_SMALL == TRUE]
, na.rm = TRUE)
### HABIT_USGS----
, nt_ADNATE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ADNATE == TRUE]
, na.rm = TRUE)
, nt_STALKED = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& STALKED == TRUE]
, na.rm = TRUE)
### MOTILE2_USGS----
, nt_HIGHLY_MOTILE.1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGHLY_MOTILE.1 == TRUE]
, na.rm = TRUE)
, nt_ARAPHID = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ARAPHID == TRUE]
, na.rm = TRUE)
### DIAT_CL----
, nt_DIAT_CL_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CL == 1]
, na.rm = TRUE)
, nt_DIAT_CL_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CL == 2]
, na.rm = TRUE)
### BEN_SES----
, nt_BEN_SES_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BEN_SES == 1]
, na.rm = TRUE)
, nt_BEN_SES_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BEN_SES == 2]
, na.rm = TRUE)
### DIAT_CA----
, nt_DIAT_CA_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CA == 1]
, na.rm = TRUE)
, nt_DIAT_CA_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CA == 2]
, na.rm = TRUE)
### DIAT_COND----
, nt_DIAT_COND_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_COND == 1]
, na.rm = TRUE)
, nt_DIAT_COND_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_COND == 2]
, na.rm = TRUE)
### DIATAS----
, nt_DIATAS_TN_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TN == 1]
, na.rm = TRUE)
, nt_DIATAS_TN_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TN == 2]
, na.rm = TRUE)
, nt_DIATAS_TP_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TP == 1]
, na.rm = TRUE)
, nt_DIATAS_TP_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TP == 2]
, na.rm = TRUE)
### MOTILITY----
, nt_MOTILITY_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MOTILITY == 1]
, na.rm = TRUE)
, nt_MOTILITY_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MOTILITY == 2]
, na.rm = TRUE)
### NF----
, nt_NF_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NF == 1]
, na.rm = TRUE)
, nt_NF_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NF == 2]
, na.rm = TRUE)
## Percent Individuals----
### Phylo----
, pi_Achnan_Navic = 100 * sum(N_TAXA[GENUS == "Achnanthidium"
| GENUS == "Navicula"]
, na.rm = TRUE) / ni_total
### N_USGS---
, pi_HIGH_N = 100 * sum(N_TAXA[HIGH_N == TRUE]
, na.rm = TRUE) / ni_total
, pi_LOW_N = 100 * sum(N_TAXA[LOW_N == TRUE]
, na.rm = TRUE) / ni_total
### P_USGS---
, pi_HIGH_P = 100 * sum(N_TAXA[HIGH_P == TRUE]
, na.rm = TRUE) / ni_total
, pi_LOW_P = 100 * sum(N_TAXA[LOW_P == TRUE]
, na.rm = TRUE) / ni_total
### BC_USGS---
, pi_BC_1 = 100 * sum(N_TAXA[BC_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_2 = 100 * sum(N_TAXA[BC_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_3 = 100 * sum(N_TAXA[BC_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_4 = 100 * sum(N_TAXA[BC_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_5 = 100 * sum(N_TAXA[BC_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_12 = 100 * sum(N_TAXA[BC_1 == TRUE
| BC_2 == TRUE]
, na.rm = TRUE) / ni_total
### PT_USGS---
, pi_PT_1 = 100 * sum(N_TAXA[PT_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_2 = 100 * sum(N_TAXA[PT_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_3 = 100 * sum(N_TAXA[PT_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_4 = 100 * sum(N_TAXA[PT_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_5 = 100 * sum(N_TAXA[PT_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_45 = 100 * sum(N_TAXA[PT_4 == TRUE
| PT_5 == TRUE]
, na.rm = TRUE) / ni_total
### SALINITY_USGS---
, pi_SALINITY_1 = 100 * sum(N_TAXA[SALINITY_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_2 = 100 * sum(N_TAXA[SALINITY_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_3 = 100 * sum(N_TAXA[SALINITY_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_4 = 100 * sum(N_TAXA[SALINITY_4 == TRUE]
, na.rm = TRUE) / ni_total
### O_USGS---
, pi_O_1 = 100 * sum(N_TAXA[O_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_2 = 100 * sum(N_TAXA[O_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_3 = 100 * sum(N_TAXA[O_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_4 = 100 * sum(N_TAXA[O_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_5 = 100 * sum(N_TAXA[O_5 == TRUE]
, na.rm = TRUE) / ni_total
### HABITAT_USGS---
, pi_SESTONIC_HABIT = 100 * sum(N_TAXA[SESTONIC_HABIT == TRUE]
, na.rm = TRUE) / ni_total
, pi_BENTHIC_HABIT = 100 * sum(N_TAXA[BENTHIC_HABIT == TRUE]
, na.rm = TRUE) / ni_total
### BAHLS_USGS---
, pi_BAHLS_1 = 100 * sum(N_TAXA[BAHLS_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BAHLS_2 = 100 * sum(N_TAXA[BAHLS_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BAHLS_3 = 100 * sum(N_TAXA[BAHLS_3 == TRUE]
, na.rm = TRUE) / ni_total
### TROPHIC_USGS---
, pi_TROPHIC_1 = 100 * sum(N_TAXA[TROPHIC_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_2 = 100 * sum(N_TAXA[TROPHIC_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_3 = 100 * sum(N_TAXA[TROPHIC_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_4 = 100 * sum(N_TAXA[TROPHIC_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_5 = 100 * sum(N_TAXA[TROPHIC_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_6 = 100 * sum(N_TAXA[TROPHIC_6 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_7 = 100 * sum(N_TAXA[TROPHIC_7 == TRUE]
, na.rm = TRUE) / ni_total
### SAP_USGS----
, pi_SAP_1 = 100 * sum(N_TAXA[SAP_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_2 = 100 * sum(N_TAXA[SAP_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_3 = 100 * sum(N_TAXA[SAP_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_4 = 100 * sum(N_TAXA[SAP_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_5 = 100 * sum(N_TAXA[SAP_5 == TRUE]
, na.rm = TRUE) / ni_total
### N_FIXER_USGS----
, pi_NON_N_FIXER = 100 * sum(N_TAXA[NON_N_FIXER == TRUE]
, na.rm = TRUE) / ni_total
, pi_N_FIXER = 100 * sum(N_TAXA[N_FIXER == TRUE]
, na.rm = TRUE) / ni_total
### MOTILITY_USGS----
, pi_HIGHLY_MOTILE = 100 * sum(N_TAXA[HIGHLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_MODERATELY_MOTILE = 100 * sum(N_TAXA[MODERATELY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_NON_MOTILE = 100 * sum(N_TAXA[NON_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_SLIGHTLY_MOTILE = 100 * sum(N_TAXA[SLIGHTLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_WEAKLY_MOTILE = 100 * sum(N_TAXA[WEAKLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
### SIZE_USGS----
, pi_BIG = 100 * sum(N_TAXA[BIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_SMALL = 100 * sum(N_TAXA[SMALL == TRUE]
, na.rm = TRUE) / ni_total
, pi_MEDIUM = 100 * sum(N_TAXA[MEDIUM == TRUE]
, na.rm = TRUE) / ni_total
, pi_VERY_BIG = 100 * sum(N_TAXA[VERY_BIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_VERY_SMALL = 100 * sum(N_TAXA[VERY_SMALL == TRUE]
, na.rm = TRUE) / ni_total
### HABIT_USGS----
, pi_ADNATE = 100 * sum(N_TAXA[ADNATE == TRUE]
, na.rm = TRUE) / ni_total
, pi_STALKED = 100 * sum(N_TAXA[STALKED == TRUE]
, na.rm = TRUE) / ni_total
### MOTILE2_USGS----
, pi_HIGHLY_MOTILE.1 = 100 * sum(N_TAXA[HIGHLY_MOTILE.1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_ARAPHID = 100 * sum(N_TAXA[ARAPHID == TRUE]
, na.rm = TRUE) / ni_total
### DIAT_CL----
, pi_DIAT_CL_1 = 100 * sum(N_TAXA[DIAT_CL == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_CL_1_ASSR = 100 * (asin(sqrt(pi_DIAT_CL_1 / 100)))
, pi_DIAT_CL_2 = 100 * sum(N_TAXA[DIAT_CL == 2]
, na.rm = TRUE) / ni_total
### BEN_SES----
, pi_BEN_SES_1 = 100 * sum(N_TAXA[BEN_SES == 1]
, na.rm = TRUE) / ni_total
, pi_BEN_SES_2 = 100 * sum(N_TAXA[BEN_SES == 2]
, na.rm = TRUE) / ni_total
### DIAT_CA----
, pi_DIAT_CA_1 = 100 * sum(N_TAXA[DIAT_CA == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_CA_2 = 100 * sum(N_TAXA[DIAT_CA == 2]
, na.rm = TRUE) / ni_total
### DIAT_COND----
, pi_DIAT_COND_1 = 100 * sum(N_TAXA[DIAT_COND == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_COND_2 = 100 * sum(N_TAXA[DIAT_COND == 2]
, na.rm = TRUE) / ni_total
### DIATAS----
, pi_DIATAS_TN_1 = 100 * sum(N_TAXA[DIATAS_TN == 1]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TN_2 = 100 * sum(N_TAXA[DIATAS_TN == 2]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TP_1 = 100 * sum(N_TAXA[DIATAS_TP == 1]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TP_2 = 100 * sum(N_TAXA[DIATAS_TP == 2]
, na.rm = TRUE) / ni_total
### MOTILITY----
, pi_MOTILITY_1 = 100 * sum(N_TAXA[MOTILITY == 1]
, na.rm = TRUE) / ni_total
, pi_MOTILITY_2 = 100 * sum(N_TAXA[MOTILITY == 2]
, na.rm = TRUE) / ni_total
### NF----
, pi_NF_1 = 100 * sum(N_TAXA[NF == 1]
, na.rm = TRUE) / ni_total
, pi_NF_2 = 100 * sum(N_TAXA[NF == 2]
, na.rm = TRUE) / ni_total
## Percent of Taxa----
### Phylo----
, pt_Achnan_Navic = 100 * nt_Achnan_Navic / nt_total
### N_USGS----
, pt_HIGH_N = 100 * nt_HIGH_N / nt_total
, pt_LOW_N = 100 * nt_LOW_N / nt_total
### P_USGS----
, pt_HIGH_P = 100 * nt_HIGH_P / nt_total
, pt_LOW_P = 100 * nt_LOW_P / nt_total
### BC_USGS----
, pt_BC_1 = 100 * nt_BC_1 / nt_total
, pt_BC_2 = 100 * nt_BC_2 / nt_total
, pt_BC_3 = 100 * nt_BC_3 / nt_total
, pt_BC_4 = 100 * nt_BC_4 / nt_total
, pt_BC_5 = 100 * nt_BC_5 / nt_total
, pt_BC_12 = 100 * nt_BC_12 / nt_total
, pt_BC_12_adj = NA_real_
, pt_BC_45 = 100 * nt_BC_45 / nt_total
### PT_USGS----
, pt_PT_1 = 100 * nt_PT_1 / nt_total
, pt_PT_2 = 100 * nt_PT_2 / nt_total
, pt_PT_3 = 100 * nt_PT_3 / nt_total
, pt_PT_4 = 100 * nt_PT_4 / nt_total
, pt_PT_5 = 100 * nt_PT_5 / nt_total
, pt_PT_12 = 100 * nt_PT_12 / nt_total
### SALINITY_USGS----
, pt_SALINITY_1 = 100 * nt_SALINITY_1 / nt_total
, pt_SALINITY_2 = 100 * nt_SALINITY_2 / nt_total
, pt_SALINITY_3 = 100 * nt_SALINITY_3 / nt_total
, pt_SALINITY_4 = 100 * nt_SALINITY_4 / nt_total
, pt_SALINITY_34 = 100 * nt_SALINITY_34 / nt_total
### O_USGS----
, pt_O_1 = 100 * nt_O_1 / nt_total
, pt_O_2 = 100 * nt_O_2 / nt_total
, pt_O_3 = 100 * nt_O_3 / nt_total
, pt_O_4 = 100 * nt_O_4 / nt_total
, pt_O_5 = 100 * nt_O_5 / nt_total
, pt_O_345 = 100 * nt_O_345 / nt_total
### HABITAT_USGS----
, pt_SESTONIC_HABIT = 100 * nt_SESTONIC_HABIT / nt_total
, pt_BENTHIC_HABIT = 100 * nt_BENTHIC_HABIT / nt_total
### BAHLS_USGS----
, pt_BAHLS_1 = 100 * nt_BAHLS_1 / nt_total
, pt_BAHLS_2 = 100 * nt_BAHLS_2 / nt_total
, pt_BAHLS_3 = 100 * nt_BAHLS_3 / nt_total
### TROPHIC_USGS----
, pt_TROPHIC_1 = 100 * nt_TROPHIC_1 / nt_total
, pt_TROPHIC_2 = 100 * nt_TROPHIC_2 / nt_total
, pt_TROPHIC_3 = 100 * nt_TROPHIC_3 / nt_total
, pt_TROPHIC_4 = 100 * nt_TROPHIC_4 / nt_total
, pt_TROPHIC_5 = 100 * nt_TROPHIC_5 / nt_total
, pt_TROPHIC_6 = 100 * nt_TROPHIC_6 / nt_total
, pt_TROPHIC_7 = 100 * nt_TROPHIC_7 / nt_total
, pt_TROPHIC_12 = 100 * nt_TROPHIC_12 / nt_total
, pt_TROPHIC_456 = 100 * nt_TROPHIC_456 / nt_total
, pt_TROPHIC_56 = 100 * nt_TROPHIC_56 / nt_total
### SAP_USGS----
, pt_SAP_1 = 100 * nt_SAP_1 / nt_total
, pt_SAP_2 = 100 * nt_SAP_2 / nt_total
, pt_SAP_3 = 100 * nt_SAP_3 / nt_total
, pt_SAP_4 = 100 * nt_SAP_4 / nt_total
, pt_SAP_5 = 100 * nt_SAP_5 / nt_total
### N_FIXER_USGS----
, pt_NON_N_FIXER = 100 * nt_NON_N_FIXER / nt_total
, pt_N_FIXER = 100 * nt_N_FIXER / nt_total
### MOTILITY_USGS----
, pt_HIGHLY_MOTILE = 100 * nt_HIGHLY_MOTILE / nt_total
, pt_MODERATELY_MOTILE = 100 * nt_MODERATELY_MOTILE / nt_total
, pt_NON_MOTILE = 100 * nt_NON_MOTILE / nt_total
, pt_SLIGHTLY_MOTILE = 100 * nt_SLIGHTLY_MOTILE / nt_total
, pt_WEAKLY_MOTILE = 100 * nt_WEAKLY_MOTILE / nt_total
### SIZE_USGS----
, pt_BIG = 100 * nt_BIG / nt_total
, pt_SMALL = 100 * nt_SMALL / nt_total
, pt_MEDIUM = 100 * nt_MEDIUM / nt_total
, pt_VERY_BIG = 100 * nt_VERY_BIG / nt_total
, pt_VERY_SMALL = 100 * nt_VERY_SMALL / nt_total
### HABIT_USGS----
, pt_ADNATE = 100 * nt_ADNATE / nt_total
, pt_STALKED = 100 * nt_STALKED / nt_total
### MOTILE2_USGS----
, pt_HIGHLY_MOTILE.1 = 100 * nt_HIGHLY_MOTILE.1 / nt_total
, pt_ARAPHID = 100 * nt_ARAPHID / nt_total
### DIAT_CL----
, pt_DIAT_CL_1 = 100 * nt_DIAT_CL_1 / nt_total
, pt_DIAT_CL_2 = 100 * nt_DIAT_CL_2 / nt_total
### BEN_SES----
, pt_BEN_SES_1 = 100 * nt_BEN_SES_1 / nt_total
, pt_BEN_SES_2 = 100 * nt_BEN_SES_2 / nt_total
### DIAT_CA----
, pt_DIAT_CA_1 = 100 * nt_DIAT_CA_1 / nt_total
, pt_DIAT_CA_2 = 100 * nt_DIAT_CA_2 / nt_total
### DIAT_COND----
, pt_DIAT_COND_1 = 100 * nt_DIAT_COND_1 / nt_total
, pt_DIAT_COND_2 = 100 * nt_DIAT_COND_2 / nt_total
### DIATAS----
, pt_DIATAS_TN_1 = 100 * nt_DIATAS_TN_1 / nt_total
, pt_DIATAS_TN_2 = 100 * nt_DIATAS_TN_2 / nt_total
, pt_DIATAS_TP_1 = 100 * nt_DIATAS_TP_1 / nt_total
, pt_DIATAS_TP_2 = 100 * nt_DIATAS_TP_2 / nt_total
### MOTILITY----
, pt_MOTILITY_1 = 100 * nt_MOTILITY_1 / nt_total
, pt_MOTILITY_2 = 100 * nt_MOTILITY_2 / nt_total
### NF----
, pt_NF_1 = 100 * nt_NF_1 / nt_total
, pt_NF_2 = 100 * nt_NF_2 / nt_total
## Tolerance----
### Number of Taxa----
, nt_Sens_810 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE# DOES NOT FOLLOW NORMAL TOLVAL CONVENTION
& TOLVAL >= 8 # LOWER VALUES MORE TOLERANT (Indiana)
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_RefIndicators = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE # Diatom Indicator Species Analysis
& REF_INDICATORS == TRUE]
, na.rm = TRUE)
, nt_Tol_13 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 1# DOES NOT FOLLOW NORMAL TOLVAL CONVENTION
& TOLVAL <= 3]# LOWER VALUES MORE TOLERANT (Indiana)
, na.rm = TRUE)
### Percent of Individuals----
, pi_Sens_810 = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE) / sum(
N_TAXA[!is.na(TOLVAL)], na.rm = TRUE)
, pi_RefIndicators = 100 * sum(N_TAXA[REF_INDICATORS == TRUE], # Diatom Indicator Species Analysis
na.rm = TRUE) / ni_total
, pi_Tol_13 = 100 * sum(N_TAXA[TOLVAL >= 1 # DOES NOT FOLLOW NORMAL TOLVAL CONVENTION (Indiana)
& TOLVAL <= 3], na.rm = TRUE) / sum(
N_TAXA[!is.na(TOLVAL)], na.rm = TRUE) # LOWER VALUES MORE TOLERANT
### Percent of Taxa----
, pt_Sens_810 = 100 * nt_Sens_810 / nt_total # DOES NOT FOLLOW NORMAL TOLVAL CONVENTION (Indiana)
, pt_RefIndicators = 100 * nt_RefIndicators / nt_total
, pt_Tol_13 = 100 * nt_Tol_13 / nt_total
### Weighted Average ----
, wa_POLL_TOL = sum(N_TAXA[!is.na(POLL_TOL)]
* POLL_TOL[!is.na(POLL_TOL)
]) / sum(N_TAXA[!is.na(POLL_TOL)])
, .groups = "drop_last")##met.val.END
# Clean Up ####
# replace NA with 0
met.val[is.na(met.val)] <- 0
# subset to only metrics specified by user
if (is.null(MetricNames)) {
met.val <- met.val
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME",
"ni_total", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>% dplyr::group_by(.dots = c("SAMPLEID"
, cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val), by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# Run Time
if (verbose) {
time_end <- Sys.time()
msg <- difftime(time_end, time_start)
message(msg)
}## IF ~ verbose
# df to report back
return(df.return)
}##FUNCTION.metric.values.algae.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, coral
#'
#' @description Subfunction of metric.values for use with coral
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.coral <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.Shiny = FALSE
, verbose) {
# define pipe
`%>%` <- dplyr::`%>%`
time_start <- Sys.time()
# not carrying over from previous
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "CORAL"
boo_debug_bugs <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 18
# global variable bindings ----
INDEX_NAME <- INDEX_CLASS <- SAMPLEID <- TAXAID <- BCG_ATTR <- WEEDY <- PHYLUM <-
CLASS <- SUBCLASS <- ORDER <- FAMILY <- GENUS <- SUBGENUS <- SPECIES <- JUVENILE <-
LRBC <- TOTTRANLNGTH_M <- DIAMMAX_CM <- DIAMPERP_CM <- HEIGHT_CM <- MORPHCONVFACT <-
TOTMORT_PCT <- WEEDY_CONFIRMED <- DIAM_CM <- R2 <- CSA <- LIVETISSUE_PCT <-
LCSA <- LCSA3D_samp_m2 <- LCSA3D_BCG_att1234_m2 <- LCSA3D_LRBC_m2 <-
ncol_AcroOrbi_m2 <- nt_BCG_att123 <- nt_BCG_att1234 <- nt_total <- pcol_Acropora <-
pcol_SmallWeedy <- pt_BCG_att5 <- ncol_Acropora <- ncol_SmallWeedy <-
nt_BCG_att5 <- NULL
# QC----
## QC, Missing Cols ----
if (verbose == TRUE) {
debug_topic <- "QC, missing cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "BCG_ATTR", "WEEDY", "PHYLUM"
, "CLASS", "SUBCLASS", "ORDER", "FAMILY"
, "GENUS", "SUBGENUS", "SPECIES")
col.req_logical <- c("JUVENILE", "LRBC")
col.req_numeric <- c("TOTTRANLNGTH_M", "DIAMMAX_CM", "DIAMPERP_CM"
, "HEIGHT_CM", "MORPHCONVFACT", "TOTMORT_PCT")
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
col.req.missing_char <- col.req_character[!(col.req_character %in% toupper(names(myDF)))]
col.req.missing_log <- col.req_logical[!(col.req_logical %in% toupper(names(myDF)))]
col.req.missing_num <- col.req_numeric[!(col.req_numeric %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
num.col.req.missing_char <- length(col.req.missing_char)
num.col.req.missing_log <- length(col.req.missing_log)
num.col.req.missing_num <- length(col.req.missing_num)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {
# Create prompt for missing columns
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the BCG_ATTR field is missing all BCG-related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
#user.input <- readline(prompt=myPrompt)
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive & boo.Shiny
# any answer other than "YES" will stop the function.
if (user.input != 1) {
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
#myDF[, col.req.missing] <- NA
if (num.col.req.missing_char > 0) {
myDF[, col.req.missing_char] <- NA_character_
}
if (num.col.req.missing_log > 0) {
myDF[, col.req.missing_log] <- NA
}
if (num.col.req.missing_num > 0) {
myDF[, col.req.missing_num] <- NA_real_
}
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing)
, collapse = "\n")
, sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(myDF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, LRBC----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, LRBC"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "LRBC"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
LRBC.T <- sum(myDF$LRBC == TRUE, na.rm = TRUE)
if (LRBC.T == 0) {
warning("LRBC column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.LRBC.T.END
## QC, Juvenile----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Juvenile"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "JUVENILE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
JUVENILE.T <- sum(myDF$JUVENILE == TRUE, na.rm = TRUE)
if (JUVENILE.T == 0) {
warning("JUVENILE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.JUVENILE.T.END
## QC, Weedy----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Weedy"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "WEEDY"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
weedy_values <- c("Never", "Sometimes")
# Extract the "Weedy" column
weedy_column <- unique(myDF[, "WEEDY"])
# Check if there are any values not in the acceptable list
if (any(!weedy_column %in% weedy_values)) {
warning("WEEDY column contains unrecognized values. \n Valid values are 'Never', 'Sometimes', or'Always'. \n Other values are not recognized.")
}##IF.WEEDY.END
## QC, Mortality ----
if (any(myDF$TOTMORT_PCT > 100)) {
warning("TOTMORT_PCT column contains values outside the normal range of 0-100. \n Fix invalid values before proceeding because LCSA-based metrics will not be calculated correctly.")
}##IF.Mort.END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging----
# Convert columns to upper case
if (verbose == TRUE) {
debug_topic <- "Munging, text cols, toupper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
col2upper <- col.req_character[!(col.req_character %in%
c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS"))]
for (i in col2upper) {
myDF[, i] <- toupper(myDF[, i])
}## FOR ~ i ~ END
# Do some calcs
myDF <- myDF %>%
dplyr::mutate(WEEDY_CONFIRMED = dplyr::case_when((WEEDY == "NEVER") ~ FALSE
, (WEEDY == "SOMETIMES"
& TAXAID != "SIDERASTREA SIDEREA"
& TAXAID != "STEPHANOCOENIA INTERSEPTA"
& DIAMMAX_CM < 75) ~ TRUE
, ((TAXAID == "SIDERASTREA SIDEREA"
| TAXAID == "STEPHANOCOENIA INTERSEPTA")
& DIAMMAX_CM <= 30
& HEIGHT_CM <= 10) ~ TRUE
, ((TAXAID == "SIDERASTREA SIDEREA"
| TAXAID == "STEPHANOCOENIA INTERSEPTA")
& DIAMMAX_CM > 30
& HEIGHT_CM > 10) ~ FALSE
, TRUE ~ FALSE)
, DIAM_CM = dplyr::case_when((!is.na(DIAMPERP_CM)
& !is.na(DIAMMAX_CM))
~ as.numeric((DIAMPERP_CM + DIAMMAX_CM)/2)
, TRUE ~ as.numeric(DIAMMAX_CM))
, R2 = ((HEIGHT_CM + (DIAM_CM/2))/2)^2
, CSA = R2*MORPHCONVFACT*pi
, LIVETISSUE_PCT = 100 - TOTMORT_PCT
, LCSA = CSA * (LIVETISSUE_PCT/100)) %>%
dplyr::select(-c(R2, LIVETISSUE_PCT))
# Metric Calc----
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
# Transect width 1m
, transect_area_m2 = max(TOTTRANLNGTH_M, na.rm = TRUE) * 1
## Individuals ----
, ncol_total = dplyr::n()
, lcol_total = log(ncol_total)
## Number of Taxa ----
, nt_total = dplyr::n_distinct(TAXAID, na.rm = TRUE)
## Percent of Taxa ----
## Number of Individuals ----
, ncol_Acropora = sum(GENUS == "ACROPORA", na.rm = TRUE)
, ncol_AcroOrbi_m2 = sum((GENUS == "ACROPORA" | GENUS == "ORBICELLA")
, na.rm = TRUE) / transect_area_m2
## Percent of Individuals ----
, pcol_Acropora = 100 * ncol_Acropora / ncol_total
## BCG ----
### BCG, nt ####
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "5")]
, na.rm = TRUE)
### BCG, pt ####
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
## Surface Area ----
, LCSA3D_samp_m2 = sum(LCSA, na.rm = TRUE) / transect_area_m2
, LCSA3D_BCG_att1234_m2 = sum(LCSA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / transect_area_m2
, LCSA3D_LRBC_m2 = sum(LCSA[(LRBC == TRUE)]
, na.rm = TRUE) / transect_area_m2
## Weedy ----
### Weedy, ncol ####
, ncol_SmallWeedy = sum(WEEDY_CONFIRMED == TRUE, na.rm = TRUE)
### Weedy, pcol ####
, pcol_SmallWeedy = 100 * ncol_SmallWeedy / ncol_total
)##met.val.END
}##FUNCTION.metric.values.coral.END
leppott/BioMonTools documentation built on March 1, 2025, 7:18 a.m.
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Defines functions metric.values.coral metric.values.algae metric.values.fish metric.values.bugs metric.values
Documented in metric.values metric.values.algae metric.values.bugs metric.values.coral metric.values.fish
#' @title Calculate metric values
#'
#' @description This function calculates metric values for bugs, fish, algae
#' , and coral. Inputs are a data frame with SampleID and taxa with phylogenetic
#' and autecological information (see below for required fields by community).
#' The dplyr package is used to generate the metric values.
#'
#' @details All percent metric results are 0-100.
#'
#' No manipulations of the taxa are performed by this routine.
#' All benthic macroinvertebrate taxa should be identified to the appropriate
#' operational taxonomic unit (OTU).
#'
#' Any non-count taxa should be identified in the "Exclude" field as "TRUE".
#' These taxa will be excluded from taxa richness metrics (but will count for
#' all others).
#'
#' Any non-target taxa should be identified in the "NonTarget"
#' field as "TRUE". Non-target taxa are those that are not part of your
#' intended #' capture list; e.g., fish, herps, water column taxa, or water
#' surface taxa in a benthic sample. The target list will vary by program. The
#' non-target taxa will be removed prior to any calculations.
#'
#' Excluded taxa are ambiguous taxa (on a sample basis), i.e.,
#' the parent taxa when child taxa are present. For example, the parent taxa
#' Chironomidae would be excluded when the child taxa Tanytarsini is present.
#' Both would be excluded when Tanytarsus is present. The markExcluded function
#' can be used to populated this field.
#'
#' There are a number of required fields (see below) for metric to calculation.
#' If any fields are missing the user will be prompted as to which are missing
#' and if the user wants to continue or quit. If the user continues the missing
#' fields will be added but will be filled with zero or NA (as appropriate).
#' Any metrics based on the missing fields will not be valid.
#'
#' A future update may turn these fields into function parameters. This would
#' allow the user to tweak the function inputs to match their data rather than
#' having to update their data to match the function.
#'
#' Required fields, all communities:
#'
#' * SAMPLEID (character or number, must be unique)
#'
#' * TAXAID (character or number, must be unique)
#'
#' * N_TAXA
#'
#' * INDEX_NAME
#'
#' * INDEX_CLASS (BCG or MMI site category; e.g., for BCG PacNW valid values
#' are "hi" or "lo")
#'
#' Additional Required fields, bugs:
#'
#' * EXCLUDE (valid values are TRUE and FALSE)
#'
#' * NONTARGET (valid values are TRUE and FALSE)
#'
#' * PHYLUM, SUBPHYLUM, CLASS, SUBCLASS, INFRAORDER, ORDER, FAMILY, SUBFAMILY,
#' TRIBE, GENUS
#'
#' * FFG, HABIT, LIFE_CYCLE, TOLVAL, BCG_ATTR, THERMAL_INDICATOR, FFG2, TOLVAL2,
#' LONGLIVED, NOTEWORTHY, HABITAT, UFC, ELEVATION_ATTR, GRADIENT_ATTR,
#' WSAREA_ATTR, HABSTRUCT
#'
#' Additional Required fields, fish:
#'
#' * N_ANOMALIES
#'
#' * SAMP_BIOMASS (biomass total for sample, funciton uses max in case entered
#' for all taxa in sample)
#'
#' * NATIVE: NATIVE or other text values
#'
#' * DA_MI2, SAMP_WIDTH_M, SAMP_LENGTH_M, , TYPE, TOLER, TROPHIC, SILT,
#' FAMILY, GENUS, HYBRID, BCG_ATTR, THERMAL_INDICATOR, ELEVATION_ATTR,
#' GRADIENT_ATTR, WSAREA_ATTR, REPRODUCTION, HABITAT, CONNECTIVITY, SCC
#'
#' Additional Required fields, algae:
#'
#' * EXCLUDE, NONTARGET, PHYLUM, ORDER, FAMILY, GENUS, BC_USGS, TROPHIC_USGS,
#' SAP_USGS, PT_USGS, O_USGS, SALINITY_USGS, BAHLS_USGS, P_USGS, N_USGS,
#' HABITAT_USGS, N_FIXER_USGS, MOTILITY_USGS, SIZE_USGS, HABIT_USGS,
#' MOTILE2_USGS, TOLVAL, DIATOM_ISA, DIAT_CL, POLL_TOL, BEN_SES, DIATAS_TP,
#' DIATAS_TN, DIAT_COND, DIAT_CA, MOTILITY, NF
#'
#' Valid values for fields:
#'
#' * FFG: CG, CF, PR, SC, SH
#'
#' * HABIT: BU, CB, CN, SP, SW
#'
#' * LIFE_CYCLE: UNI, SEMI, MULTI
#'
#' * THERMAL_INDICATOR: STENOC, COLD, COOL, WARM, STENOW, EURYTHERMAL
#' , COWA, NA
#'
#' * LONGLIVED: TRUE, FALSE
#'
#' * NOTEWORTHY: TRUE, FALSE
#'
#' * HABITAT: BRAC, DEPO, GENE, HEAD, RHEO, RIVE, SPEC, UNKN
#'
#' * UFC: integers 1:6 (taxonomic uncertainty frequency class)
#'
#' * ELEVATION_ATTR: LOW, HIGH
#'
#' * GRADIENT_ATTR: LOW, MOD, HIGH
#'
#' * WSAREA_ATTR: SMALL, MEDIUM, LARGE, XLARGE
#'
#' * REPRODUCTION: BROADCASTER, SIMPLE NEST, COMPLEX NEST, BEARER, MIGRATORY
#'
#' * CONNECTIVITY: TRUE, FALSE
#'
#' * SCC (Species of Conservation Concern): TRUE, FALSE
#'
#' 'Columns to keep' are additional fields in the input file that the user wants
#' retained in the output. Fields need to be those that are unique per sample
#' and not associated with the taxa. For example, the fields used in
#' qc.check(); Area_mi2, SurfaceArea, Density_m2, and Density_ft2.
#'
#' If fun.MetricNames is provided only those metrics will be returned in the
#' provided order. This variable can be used to sort the metrics per the user's
#' preferences. By default the metric names will be returned in the groupings
#' that were used for calculation.
#'
#' The fields TOLVAL2 and FFG2 are provided to allow the user to calculate
#' metrics based on alternative scenarios. For example, including both HBI and
#' NCBI where the NCBI uses a different set of tolerance values (TOLVAL2).
#'
#' If TAXAID is 'NONE' and N_TAXA is '0' then metrics **will** be calculated
#' with that record. Other values for TAXAID with N_TAXA = 0 will be removed
#' before calculations.
#'
#' For 'Oligochete' metrics either Class or Subclass is required for
#' calculation.
#'
#' The parameter boo.Shiny can be set to TRUE when accessing this function in
#' Shiny. Normally the QC check for required fields is interactive. Setting
#' boo.Shiny to TRUE will always continue. The default is FALSE.
#'
#' The parameter 'taxaid_dni' denotes taxa to be included in Do Not Include
#' (DNI) metrics but dropped from all other metrics. Only for benthic metrics.
#'
#' Breaking change from 0.5 to 0.6 with change from Index_Name to Index_Class.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @param fun.DF Data frame of taxa (list required fields)
#' @param fun.Community Community name for which to calculate metric values
#' (bugs, fish, algae, or coral)
#' @param fun.MetricNames Optional vector of metric names to be returned.
#' If none are supplied then all will be returned. Default=NULL
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param fun.cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
# @param MetricSort How metric names should be sort; NA = as is, AZ =
# alphabetical. Default = NULL.
#' @param boo.marine Should estuary/marine metrics be included.
#' Ignored if fun.MetricNames is not null. Default = FALSE.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#' @param metric_subset Subset of metrics to be generated. Internal function.
#' Default = NULL
#' @param taxaid_dni Taxa names to be included in DNI (Do Not Include) metrics
#' (n = 3) but dropped for all other metrics. Only for benthic metrics.
#' Default = NULL
#'
#' @return data frame of SampleID and metric values
#'
#' @examples
#' # Example 1, data already in R
#'
#' df_metric_values_bugs <- metric.values(data_benthos_PacNW, "bugs")
#'
#' \dontrun{
#' # View Results
#' View(df_metric_values_bugs)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 2, data from Excel
#'\dontrun{
#' # Packages
#' library(readxl)
#' library(reshape2)
#'
#' df_samps_bugs <- read_excel(system.file("extdata/Data_Benthos.xlsx"
#' , package = "BioMonTools")
#' , guess_max = 10^6)
#'
#' # Columns to keep
#' myCols <- c("Area_mi2", "SurfaceArea", "Density_m2", "Density_ft2")
#'
#' # Run Function
#' df_metric_values_bugs <- metric.values(df_samps_bugs[1:100, ]
#' , "bugs"
#' , fun.cols2keep = myCols)
#'
#' # View Results
#' View(df_metric_values_bugs)
#' }
#'
#' # Get data in long format so can QC results more easily
#' df_long <- melt(df_metric_values_bugs, id.vars = c("SAMPLEID"
#' , "INDEX_NAME"
#' , "INDEX_CLASS"
#' , toupper(myCols))
#' , variable.name = "METRIC_NAME"
#' , value.name = "METRIC_VALUE")
#'
#'\dontrun{
#' # Save Results
#' write.table(df_long, file.path(tempdir(), "metric.values.tsv")
#' , col.names = TRUE, row.names = FALSE, sep = "\t")
#'
#' # DataExplorer Report
#' library(DataExplorer)
#' create_report(df_metric_values_bugs
#' , output_file = file.path(tempdir()
#' , "DataExplorer_Report_MetricValues.html"))
#' create_report(df_samps_bugs
#' , output_file = file.path(tempdir()
#' , "DataExplorer_Report_BugSamples.html"))
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 3, specific metrics or metrics in a specific order
#' ## reuse df_samps_bugs from above
#'
#' # metric names to keep (in this order)
#' myMetrics <- c("ni_total", "nt_EPT", "nt_Ephem", "pi_tv_intol", "pi_Ephem"
#' , "nt_ffg_scrap", "pi_habit_climb")
#'
#' # Run Function
#' df_metric_values_bugs_myMetrics <- metric.values(df_samps_bugs, "bugs"
#' , fun.MetricNames = myMetrics)
#'\dontrun{
#' # View Results
#' View(df_metric_values_bugs_myMetrics)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 4, fish metrics
#'
#' df_metric_values_fish <- metric.values(data_fish_MBSS, "fish")
#'
#'\dontrun{
#' # View Results
#' View(df_metric_values_fish)
#' }
#'
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # Example 5, periphyton (algae) metrics
#'
#' # df_metric_values_periphyton <- metric.values(data_diatom_mmi_dev, "algae")
#'
#'\dontrun{
#' # View Results
# # View(df_metric_values_periphyton)
#' }
#'
# #~~~~~~~~~~~~~~~~~~~~~~~
# # INDIANA BCG
#
# library(readxl)
# library(reshape2)
#
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_Indiana.xlsx"
# , package="BCGcalc"), sheet="R_Input")
# dim(df.samps.bugs)
# # rename some fields
# names(df.samps.bugs)
# names(df.samps.bugs)[names(df.samps.bugs)=="VisitNum"] <- "SampleID"
# names(df.samps.bugs)[names(df.samps.bugs)=="FinalID"] <- "TaxaID"
# names(df.samps.bugs)[names(df.samps.bugs)=="Count"] <- "N_Taxa"
# # Add field
# df.samps.bugs[, "INDEX_NAME"] <- "BCG.IN"
# #
# # Run Function
# myDF <- df.samps.bugs
# df.metric.values.bugs <- metric.values(myDF, "bugs")
#
# # View Results
# View(df.metric.values.bugs)
#
# # Get data in long format so can QC results more easily
# df.long <- melt(df.metric.values.bugs, id.vars=c("SAMPLEID"
# , "INDEX_NAME"
# , "INDEX_CLASS")
# , variable.name="METRIC_NAME"
# , value.name="METRIC_VALUE")
# # Save Results
# write.table(df.long, "metric.values.tsv", col.names=TRUE, row.names=FALSE
# , sep="\t")
#
# # DataExplorer Report
# library(DataExplorer)
# create_report(df.metric.values.bugs, "DataExplorer_Report_MetricValues.html")
# create_report(df.samps.bugs, "DataExplorer_Report_BugSamples.html")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# QC 20180319
#
# library(readxl)
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_PacNW.xlsx"
# , package="BCGcalc"))
# fun.DF <- df.samps.bugs
# # PREP
# fun.DF <- as.data.frame(fun.DF)
# names(fun.DF) <- toupper(names(fun.DF))
# fun.DF <- fun.DF[fun.DF[,"N_TAXA"]>0, ]
# fun.DF <- fun.DF[fun.DF[,"NONTARGET"]==FALSE,]
# fun.DF[,"INDEX_CLASS"] <- toupper(fun.DF[,"INDEX_CLASS"])
# #
# myDF <- fun.DF
# #
# # Convert values to upper case (FFG, Habit, Life_Cycle)
# myDF[, "HABIT"] <- toupper(myDF[, "HABIT"])
# myDF[, "FFG"] <- toupper(myDF[, "FFG"])
# myDF[, "LIFE_CYCLE"] <- toupper(myDF[, "LIFE_CYCLE"])
# myDF[, "THERMAL_INDICATOR"] <- toupper(myDF[, "THERMAL_INDICATOR"])
# # Add extra columns for FFG and Habit
# # (need unique values for functions in summarise)
# # each will be TRUE or FALSE
# myDF[, "HABIT_BU"] <- grepl("BU", myDF[, "HABIT"])
# myDF[, "HABIT_CB"] <- grepl("CB", myDF[, "HABIT"])
# myDF[, "HABIT_CN"] <- grepl("CN", myDF[, "HABIT"])
# myDF[, "HABIT_SP"] <- grepl("SP", myDF[, "HABIT"])
# myDF[, "HABIT_SW"] <- grepl("SW", myDF[, "HABIT"])
# myDF[, "FFG_COL"] <- grepl("CG", myDF[, "FFG"])
# myDF[, "FFG_FIL"] <- grepl("CF", myDF[, "FFG"])
# myDF[, "FFG_PRE"] <- grepl("PR", myDF[, "FFG"])
# myDF[, "FFG_SCR"] <- grepl("SC", myDF[, "FFG"])
# myDF[, "FFG_SHR"] <- grepl("SH", myDF[, "FFG"])
# myDF[, "LC_MULTI"] <- grepl("MULTI", myDF[, "LIFE_CYCLE"])
# myDF[, "LC_SEMI"] <- grepl("SEMI", myDF[, "LIFE_CYCLE"])
# myDF[, "LC_UNI"] <- grepl("UNI", myDF[, "LIFE_CYCLE"])
# myDF[, "TI_COLD"] <- grepl("COLD", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_COLDCOOL"] <- grepl("COLD_COOL", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_COOLWARM"] <- grepl("COOL_WARM", myDF[, "THERMAL_INDICATOR"])
# myDF[, "TI_WARM"] <- grepl("WARM", myDF[, "THERMAL_INDICATOR"])
# #
# `%>%` <- dplyr::`%>%`
# mySamp <- "06039CSR_Bug_2006-07-13_0"
# x <- dplyr::filter(myDF, SAMPLEID==mySamp)
# # 26 taxa
# x <- dplyr::filter(myDF, SAMPLEID==mySamp, (BCG_ATTR == "4" | BCG_ATTR == "5"
# | BCG_ATTR == "6"))
# # 22 taxa (good)
# x <- dplyr::filter(myDF, SAMPLEID==mySamp
# , (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# , (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# , (is.na(GENUS) == TRUE | GENUS!="Juga")
# , (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")
# )
# # filter works here
# # 5 taxa and 202 ind.
#
# met.val <- dplyr::summarise(dplyr::group_by(x, SAMPLEID, INDEX_NAME, INDEX_CLASS)
# # individuals #
# , ni_total=sum(N_TAXA)
# #
# , nt_NonInsArachDecaClump_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
# & (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# & (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# & (is.na(GENUS) == TRUE | GENUS!="Juga")
# & (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")]
# , na.rm = TRUE)
# #
# , pi_NonInsArachDecaClump_BCG_att456 = sum(N_TAXA[
# (is.na(CLASS)==TRUE | (CLASS != "Insecta" & CLASS != "ARACHNIDA"))
# & (is.na(ORDER) == TRUE | (ORDER != "DECAPODA" & ORDER!="RISSOOIDEA"))
# & (is.na(GENUS) == TRUE | GENUS!="Juga")
# & (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")]
# , na.rm = TRUE)
# )
# View(met.val)
#
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# DomN metric
# library(readxl)
# library(dplyr)
# df.samps.bugs <- read_excel(system.file("./extdata/Data_BCG_PacNW.xlsx"
# , package="BCGcalc"))
# myDF <- as.data.frame(df.samps.bugs)
# names(myDF) <- toupper(names(myDF))
#
#
# # arrang in descending order (SampleID and N_Taxa)
# x <- myDF %>% arrange(SampleID, desc(N_Taxa))
# #y <- x %>% top_n(2, wt=N_Taxa) # only gets 2 rows on entire DF
# y <- x %>% group_by(SampleID) %>% filter(row_number()<=5)
# a <- table(y$SampleID)
#
# X <- myDF %>% arrange(SampleID, desc(N_Taxa)) %>%
# group_by(SampleID) %>%
# filter(row_number()<=5)
# A <- table(X$SampleID)
# View(A)
#
# # then Sum N_Taxa by SampleID
#
# # too many results (i.e., those with ties)
# z <- myDF %>% group_by(SampleID) %>% top_n(5, N_Taxa)
# View(z)
# table(z$SampID)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# OLD, Remove
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# # Metrics, MBSS Index, Fish
# myIndex <- "MBSS.2005.Fish"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Fish <- as.character(droplevels(unique(
# thresh[thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Fish <- taxa_fish
# myMetric.Values.Fish <- metric.values(myDF.Fish, "fish", myMetrics.Fish)
# View(myMetric.Values.Fish)
#
# # Metrics, Index, Benthic Macroinvertebrates, genus
# # (generate values then scores)
# myIndex <- "MBSS.2005.Bugs"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Bugs.MBSS <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Bugs.MBSS <- taxa_bugs_genus
# myMetric.Values.Bugs.MBSS <- metric.values(myDF.Bugs.MBSS, "bugs", myMetrics.Bugs.MBSS)
# View(myMetric.Values.Bugs.MBSS)
#
# # Metrics, MSW Index, Benthic Macroinvertebrates, family
# myIndex <- "MSW.1999.Bugs"
# # Thresholds
# thresh <- metrics_scoring
# # get metric names for myIndex
# (myMetrics.Bugs.MSW <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# # Taxa Data
# myDF.Bugs.MSW <- taxa_bugs_family
# myMetric.Values.Bugs.MSW <- metric.values(myDF.Bugs.MSW, "bugs", myMetrics.Bugs.MSW)
# View(myMetric.Values.Bugs.MSW)
#~~~~~~~~~~~~~~~~~~~~~~~~~~
# # QC
# ## Fish
# myIndex <- "MBSS.2005.Fish"
# thresh <- metrics_scoring
# (myMetrics.Fish <- as.character(droplevels(unique(thresh
# [thresh[,"Index_Name"]==myIndex,"Metric"]))))
# myDF <- myDF.Fish
# myMetric.Values.Fish <- metric.values(myDF.Fish, "SampleID", "fish", myMetrics.Fish, TRUE)
# fun.DF <- myDF.Fish
# fun.SampID <- "SampleID"
# fun.Community <- "fish"
# fun.MetricNames <- myMetrics.Fish"
#~~~~~~
# fun.DF <- df_samps_bugs
# fun.Community <- "bugs"
# fun.MetricNames <- c("nt_total", "nt_EPT")
# boo.Adjust <- FALSE
# fun.cols2keep=NULL
# MetricNames <- fun.MetricNames
# cols2keep <- fun.cols2keep
#~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @export
metric.values <- function(fun.DF
, fun.Community
, fun.MetricNames = NULL
, boo.Adjust = FALSE
, fun.cols2keep = NULL
, boo.marine = FALSE
, boo.Shiny = FALSE
, verbose = FALSE
, metric_subset = NULL
, taxaid_dni = NULL) {
boo_debug_main <- FALSE
debug_main_num <- 0
debug_main_num_total <- 7
boo_QC <- FALSE
# QC
if (boo_QC) {
fun.DF <- data_benthos_PacNW#[, 1:32] # 598, 37
#fun.DF <- data_benthos_MBSS # 5066, 37
fun.Community <- "bugs"
fun.MetricNames <- NULL
boo.Adjust <- FALSE
fun.cols2keep <- NULL
boo.marine <- FALSE
boo.Shiny <- FALSE
verbose <- TRUE
metric_subset <- NULL
taxaid_dni <- NULL
# Create DNI sample
taxaid_dni <- "DNI"
fun.DF <- rbind(fun.DF, fun.DF[1, ])
fun.DF[nrow(fun.DF), "TaxaID"] <- taxaid_dni
tail(fun.DF)
}## boo_QC
# global variable bindings
N_TAXA <- TAXAID <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# Munge ####
if (verbose == TRUE) {
debug_topic <- "munge"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Data Munging (common to all data types)
# Convert to data.frame. Code breaks if fun.DF is a tibble.
fun.DF <- as.data.frame(fun.DF)
# convert Field Names to UPPER CASE
names(fun.DF) <- toupper(names(fun.DF))
# convert cols2keep to UPPER CASE
if (!is.null(fun.cols2keep)) {
#names(fun.cols2keep) <- toupper(fun.cols2keep)
fun.cols2keep <- toupper(fun.cols2keep)
}##IF~!is.null(fun.cols2keep)~END
# subset to upper case
if (!is.null(metric_subset)) {
metric_subset <- toupper(metric_subset)
} else {
metric_subset <- "ALL"
}##IF~!is.null(metric_subset)~END
metric_subset <- ifelse(is.na(metric_subset), NA, toupper(metric_subset))
# QC, missing cols ----
# bare minimum, applies to all communities
if (verbose == TRUE) {
debug_topic <- "QC missing cols"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ boo_debug_main
#QC, Add required fields for this part of the code
if (toupper(fun.Community) == "CORAL") {
col.req <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS")
} else {
col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "INDEX_NAME", "INDEX_CLASS")
} # end if/else
col.req.missing <- col.req[!(col.req %in% toupper(names(fun.DF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0 & interactive() == TRUE) {
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
# special condition for Shiny
# Shiny counts as interactive()==TRUE but cannot access this prompt in Shiny.
if (boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n")
, sep = "\n"))
}##IF.user.input.END
# Add missing fields
if (verbose == TRUE) {
debug_topic <- "add missing fields"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
## Add missing, Index_Name
req.name <- "INDEX_NAME"
if (req.name %in% col.req.missing) {
fun.DF[, req.name] <- "BioMonTools"
}## IF ~ req.name
## Add missing, INDEX_CLASS
req.name <- "INDEX_CLASS"
if (req.name %in% col.req.missing) {
fun.DF[, req.name] <- fun.Community
}## IF ~ req.name
## Add missing, N_Taxa
req.name <- c("SAMPLEID", "TAXAID", "N_TAXA")
if (sum(req.name %in% col.req.missing) == length(req.name)) {
req.name.missing <- req.name[req.name %in% col.req.missing]
stop(paste("Required columns missing: "
, paste(paste0(" ",req.name.missing), collapse = "\n"),sep = "\n"))
}## IF ~ req.name
## old
#fun.DF[,col.req.missing] <- NA_character_
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames:"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(fun.DF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
# Remove Count = 0 taxa unless TaxaID = NONE
if (verbose == TRUE) {
debug_topic <- "remove count 0"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
#fun.DF <- fun.DF[fun.DF[,"N_TAXA"]>0, ]
if (toupper(fun.Community) != "CORAL") {
fun.DF <- fun.DF %>% dplyr::filter(N_TAXA > 0 | TAXAID == "NONE")
}## IF ~ taxa not zero
# non-target taxa removed in community function, if appropriate
#
# SiteType to upper case
if (verbose == TRUE) {
debug_topic <- "sitetype toupper"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# fun.DF[,"INDEX_CLASS"] <- toupper(fun.DF[,"INDEX_CLASS"])
# convert community to upper case
fun.Community <- toupper(fun.Community)
# run the proper sub function
if (verbose == TRUE) {
debug_topic <- "start subfunctions"
debug_main_num <- debug_main_num + 1
msg <- paste0("debug_metval_main, "
, debug_main_num
, "/"
, debug_main_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Subfunctions ----
# Run subfunction based on community
if (fun.Community == "BUGS") {##IF.START
metric.values.bugs(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.marine = boo.marine
, boo.Shiny = boo.Shiny
, verbose = verbose
, metric_subset = metric_subset
, taxaid_dni = taxaid_dni)
} else if (fun.Community == "FISH") {
metric.values.fish(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, boo.Shiny = boo.Shiny
, verbose = verbose)
} else if (fun.Community == "ALGAE") {
metric.values.algae(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.Shiny = boo.Shiny
, verbose = verbose)
} else if (fun.Community == "CORAL") {
metric.values.coral(myDF = fun.DF
, MetricNames = fun.MetricNames
, boo.Adjust = boo.Adjust
, cols2keep = fun.cols2keep
, MetricSort = NA
, boo.Shiny = boo.Shiny
, verbose = verbose)
}##IF.END
}##FUNCTION.metric.values.START
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Bugs
#'
#' @description Subfunction of metric.values for use with Benthic
#' Macroinvertebrates
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.marine Should estuary/marine metrics be included.
#' Ignored if fun.MetricNames is not null. Default = FALSE.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#' @param metric_subset Subset of metrics to be generated. Internal function.
#' Default = NULL
#' @param taxaid_dni Taxa names to be included in DNI (Do Not Include) metrics
#' (n = 3) but dropped for all other metrics. Only for benthic metrics.
#' Default = NULL
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.bugs <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.marine = FALSE
, boo.Shiny
, verbose
, metric_subset
, taxaid_dni = NULL) {
#
# QC
boo_QC <- FALSE
if (boo_QC) {
myDF <- fun.DF
boo.Adjust <- boo.Adjust
cols2keep <- fun.cols2keep
MetricSort <- NA
boo.marine <- boo.marine
boo.Shiny <- boo.Shiny
verbose <- verbose
metric_subset <- NULL
taxaid_dni <- "DNI" #added last entry in previous function
}## IF ~ boo_QC
time_start <- Sys.time()
# not carrying over from previous?!
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "BUGS"
boo_debug_bugs <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 18
# global variable bindings ----
INDEX_NAME <- INDEX_CLASS <- SAMPLEID <- TAXAID <- N_TAXA <- EXCLUDE <-
BCG_ATTR <- NONTARGET <- LONGLIVED <- NOTEWORTHY <- TOLVAL <- TOLVAL2 <-
UFC <- ELEVATION_ATTR <- GRADIENT_ATTR <- WSAREA_ATTR <- NULL
FFG2_PRE <- TI_CORECOLD <- TI_COLD <- TI_COOL <- TI_WARM <- TI_NA <-
TI_CORECOLD_COLD <- TI_COOL_WARM <- NULL
PHYLUM <- SUBPHYLUM <- CLASS <- SUBCLASS <- INFRAORDER <- ORDER <-
FAMILY <- SUBFAMILY <- TRIBE <- GENUS <- NULL
FFG_COL <- FFG_FIL <- FFG_PRE <- FFG_SCR <- FFG_SHR <- FFG_MAH <- FFG_PIH <-
FFG_XYL <- FFG_OMN <- FFG_PAR <- HABITAT_SPEC <- HABITAT_UNKN <- NULL
ni_total <- ni_Americo <- ni_Gnorimo <- ni_EPT <- ni_Trich <- nt_Amph <-
nt_total <- nt_Bival <- nt_Coleo <- nt_COET <- nt_Deca <- nt_Dipt <-
nt_Ephem <- nt_EPT <- nt_ET <- nt_Gast <- nt_Insect <- nt_Isop <- nt_Mega <-
nt_NonIns <- nt_Nudib <- nt_Odon <- nt_OET <- nt_Oligo <- nt_Pleco <-
nt_POET <- nt_Poly <- nt_PolyNoSpion <- nt_Spion <- nt_Trich <- ni_Chiro <-
nt_Chiro <- nt_NonInsArachDeca_BCG_att456 <-
nt_NonInsArachDecaJugaRiss_BCG_att456 <- ni_dom02_NoJugaRiss_BCG_att456 <-
nt_NonIns_BCG_att456 <- nt_NonInsJugaRiss_BCG_att456 <- nt_BCG_att1m <-
nt_BCG_att12 <- nt_BCG_att1i2 <- nt_BCG_att123 <- nt_BCG_att1i23 <-
nt_BCG_att2 <- nt_BCG_att23 <- nt_BCG_att234 <- nt_BCG_att3 <-
nt_BCG_att4 <- nt_BCG_att45 <- nt_BCG_att5 <- nt_BCG_att56 <- nt_BCG_att6 <-
nt_BCG_attNA <- nt_EPT_BCG_att123 <- nt_ti_c <- nt_ti_cc <- nt_ti_cw <-
nt_ti_w <- nt_tv_intol <- nt_tv_intol4 <- nt_tv_toler <- nt_tv_ntol <-
nt_tv_stol <- nt_ffg_col <- nt_ffg_filt <- nt_ffg_pred <- nt_habitat_brac <-
nt_habitat_depo <- nt_habitat_gene <- nt_habitat_head <- nt_habitat_rheo <-
nt_habitat_rive <- nt_habitat_spec <- nt_habitat_unkn <- nt_BCG_att1 <-
nt_BCG_att1i <- HABITAT_BRAC <- HABITAT_DEPO <- HABITAT_GENE <-
HABITAT_HEAD <- HABITAT_RHEO <- HABITAT_RIVE <- HABIT_BU <- HABIT_CB <-
HABIT_CN <- HABIT_SP <- HABIT_SW <- LC_MULTI <- LC_SEMI <- LC_UNI <-
ni_dom02 <- ni_dom03 <- ni_dom04 <- ni_dom05 <- ni_dom06 <- ni_dom07 <-
ni_dom08 <- ni_dom09 <- ni_dom10 <- nt_ffg_scrap <- nt_ffg_shred <-
nt_habit_burrow <- nt_habit_climb <- nt_habit_cling <- nt_habit_sprawl <-
nt_habit_swim <- nt_volt_multi <- nt_volt_semi <- nt_volt_uni <- x_Shan_e <-
NULL
nt_ffg_mah <- nt_ffg_pih <- nt_ffg_xyl <- nt_ffg_omn <- nt_ffg_par <-
pi_ffg_mah <- pi_ffg_pih <- pi_ffg_xyl <- pi_ffg_omn <- pi_ffg_par <-
pt_ffg_mah <- pt_ffg_pih <- pt_ffg_xyl <- pt_ffg_omn <- pt_ffg_par <- NULL
nt_ECT <- pi_ECT <- pt_ECT <- NULL
WSAREA_S <- WSAREA_M <- WSAREA_L <- WSAREA_XL <- NULL
ELEVATION_HIGH <- ELEVATION_LOW <- GRADIENT_HIGH <- GRADIENT_LOW <-
GRADIENT_MOD <- TI_EURY <- nt_BCG_att456 <- nt_EPT_BCG_att1i23 <-
nt_NonInsTrombJuga_BCG_att456 <- nt_Tromb <- nt_ti_cold <- nt_ti_cool <-
nt_ti_cool_warm <- nt_ti_corecold <- nt_ti_corecold_cold <- nt_ti_eury <-
nt_ti_na <- nt_ti_warm <- NULL
HABSTRUCT <- HABSTRUCT_CS <- HABSTRUCT_NF <- HABSTRUCT_RM <- HABSTRUCT_SG <-
nt_Hempit <- pi_Hemipt <- pt_Hemipt <- nt_oneind <- NULL
nt_BCG_att4b <- pi_BCG_att4b <- pt_BCG_att4b <- nt_BCG_att1i234b5 <-
pi_BCG_att1i234b5 <- pt_BCG_att1i234b5 <- nt_BCG_att1i234w5 <-
pi_BCG_att1i234w5 <- pt_BCG_att1i234w5 <- NULL
nt_Hemipt <- nt_dni <- pi_dni <- pt_dni <- NULL
pi_EphemNoBaeTri <- nt_EphemNoBaeTri <- nt_COETNoBraBaeHydTri <- x_BCICTQa <-
NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC----
## QC, Missing Cols ----
if (verbose == TRUE) {
debug_topic <- "QC, missing cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
, "PHYLUM", "SUBPHYLUM", "CLASS", "SUBCLASS", "INFRAORDER"
, "ORDER", "FAMILY", "SUBFAMILY", "TRIBE", "GENUS"
, "FFG", "HABIT", "LIFE_CYCLE"
, "BCG_ATTR", "THERMAL_INDICATOR"
, "FFG2", "HABITAT", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR", "HABSTRUCT"
, "BCG_ATTR2")
col.req_logical <- c("EXCLUDE", "NONTARGET"
, "LONGLIVED", "NOTEWORTHY", "AIRBREATHER")
col.req_numeric <- c("N_TAXA", "TOLVAL", "TOLVAL2", "UFC")
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
# col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "EXCLUDE", "INDEX_NAME"
# , "INDEX_CLASS", "NONTARGET", "PHYLUM", "SUBPHYLUM", "CLASS"
# , "SUBCLASS", "INFRAORDER", "ORDER", "FAMILY", "SUBFAMILY"
# , "TRIBE", "GENUS", "FFG", "HABIT", "LIFE_CYCLE", "TOLVAL"
# , "BCG_ATTR", "THERMAL_INDICATOR", "LONGLIVED", "NOTEWORTHY"
# , "FFG2", "TOLVAL2", "HABITAT", "UFC", "ELEVATION_ATTR"
# , "GRADIENT_ATTR", "WSAREA_ATTR")
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
col.req.missing_char <- col.req_character[!(col.req_character %in% toupper(names(myDF)))]
col.req.missing_log <- col.req_logical[!(col.req_logical %in% toupper(names(myDF)))]
col.req.missing_num <- col.req_numeric[!(col.req_numeric %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
num.col.req.missing_char <- length(col.req.missing_char)
num.col.req.missing_log <- length(col.req.missing_log)
num.col.req.missing_num <- length(col.req.missing_num)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {
# Create prompt for missing columns
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
#user.input <- readline(prompt=myPrompt)
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive & boo.Shiny
# # special condition for Shiny
# # Shiny counts as interactive()==TRUE locally
# but cannot access this prompt in Shiny.
# if (boo.Shiny==FALSE) {
# user.input <- utils::menu(c("YES", "NO"), title=myPrompt)
# } else {
# message(myPrompt)
# message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
# user.input <- 1
# }## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
#myDF[, col.req.missing] <- NA
if (num.col.req.missing_char > 0) {
myDF[, col.req.missing_char] <- NA_character_
}
if (num.col.req.missing_log > 0) {
myDF[, col.req.missing_log] <- NA
}
if (num.col.req.missing_num > 0) {
myDF[, col.req.missing_num] <- NA_real_
}
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing)
, collapse = "\n")
, sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(myDF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Exclude"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "EXCLUDE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {
warning("EXCLUDE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, NonTarget----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, NonTarget"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "NONTARGET"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
NonTarget.F <- sum(myDF$NONTARGET == FALSE, na.rm = TRUE)
if (NonTarget.F == 0) {
warning("NONTARGET column does not have any FALSE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, TolVal----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, TolVal"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "TOLVAL"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
TolVal_Char_NA <- myDF[, "TOLVAL"] == "NA"
# Fails with mix of NA and "NA", rework
TolVal_Char_NA <- TolVal_Char_NA == TRUE & !is.na(TolVal_Char_NA)
if (sum(TolVal_Char_NA, na.rm = TRUE) > 0) {
#myDF[TolVal_Char_NA, "TOLVAL"] <- NA
myDF[, "TOLVAL"] <- as.numeric(myDF[, "TOLVAL"])
# will give a warning - NAs introduced by coercion
msg <- "Updated col class; TOLVAL to numeric"
message(msg)
}##IF ~ TOLVAL ~ END
## QC, TolVal2----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, TolVal2"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "TOLVAL2"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
TolVal2_Char_NA <- myDF[, "TOLVAL2"] == "NA"
if (sum(TolVal2_Char_NA, na.rm = TRUE) > 0) {
myDF[TolVal2_Char_NA, "TOLVAL2"] <- NA
myDF[, "TOLVAL2"] <- as.numeric(myDF[, "TOLVAL2"])
msg <- "Updated col class; TOLVAL2 to numeric"
message(msg)
}##IF ~ TOLVAL2 ~ END
## QC, UFC----
# need as numeric, if have "NA" as character it fails
if (verbose == TRUE) {
debug_topic <- "QC, cols, numeric, UFC"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "UFC"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
UFC_Char_NA <- myDF[, "UFC"] == "NA"
if (sum(UFC_Char_NA, na.rm = TRUE) > 0) {
myDF[UFC_Char_NA, "UFC"] <- NA
myDF[, "UFC"] <- as.numeric(myDF[, "UFC"])
msg <- "Updated col class; UFC to numeric"
message(msg)
}##IF ~ UFC ~ END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging ####
if (verbose == TRUE) {
debug_topic <- "Munging"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Remove NonTarget Taxa (added back 20200715, missing since 20200224)
# Function fails if all NA (e.g., column was missing) (20200724)
if (verbose == TRUE) {
debug_topic <- "Munging, NonTarget"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "NONTARGET"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
myDF <- dplyr::filter(myDF, NONTARGET != TRUE | is.na(NONTARGET))
# # Convert columns to upper case (Phylo, FFG, Habit, Life_Cycle)
if (verbose == TRUE) {
debug_topic <- "Munging, text cols, toupper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# col2upper <- c("TAXAID", "PHYLUM", "SUBPHYLUM", "CLASS", "SUBCLASS"
# , "INFRAORDER", "ORDER", "FAMILY", "SUBFAMILY"
# , "TRIBE", "GENUS"
# , "HABIT", "FFG", "LIFE_CYCLE", "THERMAL_INDICATOR"
# , "FFG2", "HABITAT"
# , "ELEVATION_ATTR", "GRADIENT_ATTR", "WSAREA_ATTR")
col2upper <- col.req_character[!(col.req_character %in%
c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS"))]
# #myDF <- apply(myDF[, col2upper], 2, toupper)
for (i in col2upper) {
myDF[, i] <- toupper(myDF[, i])
}## FOR ~ i ~ END
# use toupper() earlier, don't need
# removed as causing issues with shiny.io with some missing fields
# 2022-02-21, previous no longer present, redo here (all fields now present)
# Add extra columns for some fields
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "CN, CB" is both "CN" and "CB"
if (verbose == TRUE) {
debug_topic <- "Munging, TF"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Remove white space
myDF[, "HABIT"] <- gsub(" ","", myDF[, "HABIT"])
myDF[, "FFG"] <- gsub(" ","", myDF[, "FFG"])
myDF[, "LIFE_CYCLE"] <- gsub(" ","", myDF[, "LIFE_CYCLE"])
myDF[, "FFG2"] <- gsub(" ","", myDF[, "FFG2"])
myDF[, "THERMAL_INDICATOR"] <- gsub(" ","", myDF[, "THERMAL_INDICATOR"])
myDF[, "HABSTRUCT"] <- gsub(" ","", myDF[, "HABSTRUCT"])
myDF[, "ELEVATION_ATTR"] <- gsub(" ","", myDF[, "ELEVATION_ATTR"])
myDF[, "GRADIENT_ATTR"] <- gsub(" ","", myDF[, "GRADIENT_ATTR"])
myDF[, "WSAREA_ATTR"] <- gsub(" ","", myDF[, "WSAREA_ATTR"])
# code new columns
## match, any
myDF[, "HABIT_BU"] <- grepl("BU", myDF[, "HABIT"])
myDF[, "HABIT_CB"] <- grepl("CB", myDF[, "HABIT"])
myDF[, "HABIT_CN"] <- grepl("CN", myDF[, "HABIT"])
myDF[, "HABIT_SK"] <- grepl("SK", myDF[, "HABIT"])
myDF[, "HABIT_SP"] <- grepl("SP", myDF[, "HABIT"])
myDF[, "HABIT_SW"] <- grepl("SW", myDF[, "HABIT"])
myDF[, "FFG_COL"] <- grepl("(CG|GC)", myDF[, "FFG"])
myDF[, "FFG_FIL"] <- grepl("(CF|FC)", myDF[, "FFG"])
myDF[, "FFG_PRE"] <- grepl("PR", myDF[, "FFG"])
myDF[, "FFG_SCR"] <- grepl("SC", myDF[, "FFG"])
myDF[, "FFG_SHR"] <- grepl("SH", myDF[, "FFG"])
myDF[, "FFG_MAH"] <- grepl("MH", myDF[, "FFG"]) # macrophyte herbivore
myDF[, "FFG_OMN"] <- grepl("OM", myDF[, "FFG"])
myDF[, "FFG_PAR"] <- grepl("PA", myDF[, "FFG"])
myDF[, "FFG_PIH"] <- grepl("PH", myDF[, "FFG"])
myDF[, "FFG_XYL"] <- grepl("XY", myDF[, "FFG"])
myDF[, "LC_MULTI"] <- grepl("MULTI", myDF[, "LIFE_CYCLE"])
myDF[, "LC_SEMI"] <- grepl("SEMI", myDF[, "LIFE_CYCLE"])
myDF[, "LC_UNI"] <- grepl("UNI", myDF[, "LIFE_CYCLE"])
myDF[, "FFG2_PRE"] <- grepl("PR", myDF[, "FFG2"])
myDF[, "TI_STENOCOLD"] <- grepl("STENOC", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COLD"] <- grepl("COLD", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COOL"] <- grepl("COOL", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_WARM"] <- grepl("WARM", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_STENOWARM"] <- grepl("STENOW", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_EURY"] <- grepl("EURYTHERMAL", myDF[, "THERMAL_INDICATOR"])
myDF[, "TI_COWA"] <- grepl("COWA", myDF[,"THERMAL_INDICATOR"])
myDF[, "HS_CS"] <- grepl("CS", myDF[, "HABSTRUCT"])
myDF[, "HS_NF"] <- grepl("NF", myDF[, "HABSTRUCT"])
myDF[, "HS_RM"] <- grepl("RM", myDF[, "HABSTRUCT"])
myDF[, "HS_SG"] <- grepl("SG", myDF[, "HABSTRUCT"])
## match, exact only
myDF[, "TI_NA"] <- is.na(myDF[, "THERMAL_INDICATOR"]) |
myDF[, "THERMAL_INDICATOR"] == ""
myDF[, "HABITAT_BRAC"] <- "BRAC" == myDF[, "HABITAT"]
myDF[, "HABITAT_DEPO"] <- "DEPO" == myDF[, "HABITAT"]
myDF[, "HABITAT_GENE"] <- "GENE" == myDF[, "HABITAT"]
myDF[, "HABITAT_HEAD"] <- "HEAD" == myDF[, "HABITAT"]
myDF[, "HABITAT_LENT"] <- "LENT" == myDF[, "HABITAT"]
myDF[, "HABITAT_LOTI"] <- "LOTI" == myDF[, "HABITAT"]
myDF[, "HABITAT_RHEO"] <- "RHEO" == myDF[, "HABITAT"]
myDF[, "HABITAT_RIVE"] <- "RIVE" == myDF[, "HABITAT"]
myDF[, "HABITAT_SPEC"] <- "SPEC" == myDF[, "HABITAT"]
myDF[, "HABITAT_TERR"] <- "TERR" == myDF[, "HABITAT"]
myDF[, "HABITAT_UNKN"] <- "UNKN" == myDF[, "HABITAT"]
myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"]
myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"]
myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"]
myDF[, "WSAREA_S"] <- "SMALL" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_M"] <- "MEDIUM" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_L"] <- "LARGE" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_XL"] <- "XLARGE" == myDF[, "WSAREA_ATTR"]
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# skip above in testing
# myDF[, "HABIT_BU"] <- FALSE
# myDF[, "HABIT_CB"] <- FALSE
# myDF[, "HABIT_CN"] <- FALSE
# myDF[, "HABIT_SP"] <- FALSE
# myDF[, "HABIT_SW"] <- FALSE
# myDF[, "FFG_COL"] <- FALSE
# myDF[, "FFG_FIL"] <- FALSE
# myDF[, "FFG_PRE"] <- FALSE
# myDF[, "FFG_SCR"] <- FALSE
# myDF[, "FFG_SHR"] <- FALSE
# myDF[, "LC_MULTI"] <- FALSE
# myDF[, "LC_SEMI"] <- FALSE
# myDF[, "LC_UNI"] <- FALSE
# # exact matches only
# myDF[, "TI_COLD"] <- FALSE
# myDF[, "TI_COLDCOOL"] <- FALSE
# myDF[, "TI_COOLWARM"] <- FALSE
# myDF[, "TI_WARM"] <- FALSE
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Calculate Metrics (could have used pipe, %>%)
# met.val <- myDF %>%
# dplyr::group_by(SAMPLEID, INDEX_NAME, INDEX_CLASS) %>%
# dplyr::summarise(ni_total=sum(N_TAXA)
# , nt_total=dplyr::n_distinct(TAXAID[EXCLUDE != TRUE], na.rm = TRUE)
# , ni_max= max(N_TAXA)
# , ni_dom01=dplyr::top_n(n=1, wt=N_TAXA)
# )
#https://stackoverflow.com/questions/45365484/how-to-find-top-n-descending-values-in-group-in-dplyr
# may have to create a 2nd output with domX metrics then join together.
# dom.val <- myDF %>%
# group_by(SAMPLEID, INDEX_NAME, INDEX_CLASS) %>%
# summarise(N_TAXA=n()) %>%
# top_n(n=3, wt=N_TAXA) %>%
# arrange()
# https://groups.google.com/forum/#!topic/manipulatr/ZzohinbNsJc
# X <- myDF %>% arrange(SampleID, desc(N_Taxa)) %>%
# group_by(SampleID) %>%
# filter(row_number()<=5)
# Create Dominant N ####
# Create df for Top N (without ties)
if (verbose == TRUE) {
debug_topic <- "Munging, Dom"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# DF for dom so same taxa get combined
# 2023-10-24, remove taxaid_dni
myDF_dom <- dplyr::summarise(dplyr::group_by(myDF
, INDEX_NAME
, INDEX_CLASS
, SAMPLEID
, TAXAID
, GENUS
, ORDER
, BCG_ATTR)
, N_TAXA = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last") %>%
dplyr::filter(!TAXAID %in% taxaid_dni) # doesn't work if do first
df.dom01 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom02 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom03 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 3)
df.dom04 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 4)
df.dom05 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 5)
df.dom06 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 6)
df.dom07 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 7)
df.dom08 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 8)
df.dom09 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 9)
df.dom10 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 10)
df.dom02_NoJugaRiss_BCG_att456 <- dplyr::arrange(myDF_dom, SAMPLEID
, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter((is.na(GENUS) == TRUE | GENUS != "JUGA")
& (is.na(ORDER) == TRUE | ORDER != "RISSOOIDEA")
& (BCG_ATTR == "4" | BCG_ATTR == "5" | BCG_ATTR == "6")) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom01_BCG_att4 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(BCG_ATTR == "4") %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom01_BCG_att5 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(BCG_ATTR == "5") %>%
dplyr::filter(dplyr::row_number() <= 1)
# Summarise Top N
df.dom01.sum <- dplyr::summarise(dplyr::group_by(df.dom01
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02.sum <- dplyr::summarise(dplyr::group_by(df.dom02
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom03.sum <- dplyr::summarise(dplyr::group_by(df.dom03
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom03 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom04.sum <- dplyr::summarise(dplyr::group_by(df.dom04
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom04 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom05.sum <- dplyr::summarise(dplyr::group_by(df.dom05
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom05 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom06.sum <- dplyr::summarise(dplyr::group_by(df.dom06
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom06 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom07.sum <- dplyr::summarise(dplyr::group_by(df.dom07
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom07 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom08.sum <- dplyr::summarise(dplyr::group_by(df.dom08
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom08 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom09.sum <- dplyr::summarise(dplyr::group_by(df.dom09
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom09 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom10.sum <- dplyr::summarise(dplyr::group_by(df.dom10
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom10 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02_NoJugaRiss_BCG_att456.sum <- dplyr::summarise(dplyr::group_by(df.dom02_NoJugaRiss_BCG_att456
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02_NoJugaRiss_BCG_att456 = sum(N_TAXA)
, .groups = "drop_last")
df.dom01_BCG_att4.sum <- dplyr::summarise(dplyr::group_by(df.dom01_BCG_att4
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_BCG_att4 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom01_BCG_att5.sum <- dplyr::summarise(dplyr::group_by(df.dom01_BCG_att5
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_BCG_att5 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# Add column of domN to main DF
myDF <- merge(myDF, df.dom01.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom03.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom04.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom05.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom06.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom07.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom08.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom09.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom10.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02_NoJugaRiss_BCG_att456.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom01_BCG_att4.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom01_BCG_att5.sum, all.x = TRUE)
# Convert NA to 0 (avoid -Inf in later calculations)
myDF[is.na(myDF[, "ni_dom02_NoJugaRiss_BCG_att456"])
, "ni_dom02_NoJugaRiss_BCG_att456"] <- 0
myDF[is.na(myDF[, "ni_dom01_BCG_att4"]), "ni_dom01_BCG_att4"] <- 0
myDF[is.na(myDF[, "ni_dom01_BCG_att5"]), "ni_dom01_BCG_att5"] <- 0
# Clean up extra Dom data frames
rm(myDF_dom)
rm(df.dom01)
rm(df.dom02)
rm(df.dom03)
rm(df.dom04)
rm(df.dom05)
rm(df.dom06)
rm(df.dom07)
rm(df.dom08)
rm(df.dom09)
rm(df.dom10)
rm(df.dom02_NoJugaRiss_BCG_att456)
rm(df.dom01_BCG_att4)
rm(df.dom01_BCG_att5)
rm(df.dom01.sum)
rm(df.dom02.sum)
rm(df.dom03.sum)
rm(df.dom04.sum)
rm(df.dom05.sum)
rm(df.dom06.sum)
rm(df.dom07.sum)
rm(df.dom08.sum)
rm(df.dom09.sum)
rm(df.dom10.sum)
rm(df.dom02_NoJugaRiss_BCG_att456.sum)
rm(df.dom01_BCG_att4.sum)
rm(df.dom01_BCG_att5.sum)
# Metric Calc -----
if (verbose == TRUE) {
debug_topic <- "Calc, metrics"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
time_start2 <- Sys.time()
# Need for metrics without taxaid_dni
myDF.dni_F <- dplyr::filter(myDF, !TAXAID %in% taxaid_dni)
if (metric_subset == "MTTI") {
## Metric Calc, MTTI ----
### met.val, DNI = FALSE----
met.val.dni_F <- dplyr::summarise(dplyr::group_by(myDF.dni_F
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
#
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
# WAopt
, x_tv2_min = min(TOLVAL2, na.rm = TRUE)
, x_tv2_max = max(TOLVAL2, na.rm = TRUE)
, .groups = "drop_last"
)## met.val.dni_F ~ END
### met.val, DNI = TRUE----
met.val.dni_T <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
#### totals ----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
#### DNI ----
, nt_dni = sum(TAXAID == "DNI", na.rm = TRUE)
, pi_dni = 100 * sum(N_TAXA[TAXAID == "DNI"]
, na.rm = TRUE) / ni_total
, pt_dni = 100 * nt_dni / nt_total
, .groups = "drop_last"
)## met.val.dni_F ~ END
### met.val, join----
cols2match <- c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS")
met_dni <- c("nt_dni", "pi_dni", "pt_dni")
met.val <- dplyr::left_join(met.val.dni_F
, met.val.dni_T[, c(cols2match, met_dni)])
} else {
## Metric Calc, ALL ----
### met.val, DNI = FALSE----
met.val.dni_F <- dplyr::summarise(dplyr::group_by(myDF.dni_F
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
### Individuals ####
, ni_total = sum(N_TAXA, na.rm = TRUE)
, ni_totalNoDeca = sum(N_TAXA[is.na(ORDER) == TRUE |
ORDER != "DECAPODA"], na.rm = TRUE)
, li_total = log(ni_total)
, ni_Chiro = sum(N_TAXA[FAMILY == "CHIRONOMIDAE"], na.rm = TRUE)
, ni_Dipt = sum(N_TAXA[ORDER == "DIPTERA"], na.rm = TRUE)
, ni_EPT = sum(N_TAXA[ORDER == "EPHEMEROPTERA" |
ORDER == "PLECOPTERA" |
ORDER == "TRICHOPTERA"], na.rm = TRUE)
, ni_Trich = sum(N_TAXA[ORDER == "TRICHOPTERA"], na.rm = TRUE)
, ni_Americo = sum(N_TAXA[GENUS == "AMERICOROPHIUM"], na.rm = TRUE)
, ni_Gnorimo = sum(N_TAXA[GENUS == "GNORIMOSPHAEROMA"], na.rm = TRUE)
, ni_brackish = ni_Americo + ni_Gnorimo
, ni_Ramello = sum(N_TAXA[GENUS == "RAMELLOGAMMARUS"], na.rm = TRUE)
### Phylo ####
#### nt_phylo ----
# account for "NONE" in nt_total, should be the only 0 N_TAXA
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
, nt_Amph = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "AMPHIPODA"]
, na.rm = TRUE)
, nt_Bival = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "BIVALVIA"]
, na.rm = TRUE)
, nt_Capit = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CAPITELLIDAE"]
, na.rm = TRUE)
, nt_Caridea = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& INFRAORDER == "CARIDEA"]
, na.rm = TRUE)
#, nt_Chiro ## in special Chironomidae section
, nt_Coleo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, nt_COET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_COETNoBraBaeHydTri = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "BRACHYCENTRUS")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE)
, nt_CruMol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE)
, nt_Deca = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "DECAPODA"]
, na.rm = TRUE)
, nt_Dipt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "DIPTERA"]
, na.rm = TRUE)
, nt_ECT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "COLEOPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_Ephem = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, nt_EphemNoBaeTri = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE)
, nt_Ephemerellid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "EPHEMERELLIDAE"]
, na.rm = TRUE)
, nt_EPT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_ET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA")]
, na.rm = TRUE)
, nt_Gast = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "GASTROPODA"]
, na.rm = TRUE)
, nt_Hemipt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "HEMIPTERA"]
, na.rm = TRUE)
, nt_Hepta = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "HEPTAGENIIDAE"]
, na.rm = TRUE)
, nt_Insect = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "INSECTA"]
, na.rm = TRUE)
, nt_Isop = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ISOPODA"]
, na.rm = TRUE)
, nt_Mega = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "MEGALOPTERA"]
, na.rm = TRUE)
, nt_Mol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"]
, na.rm = TRUE)
, nt_Nereid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "NEREIDIDAE"]
, na.rm = TRUE)
, nt_Nemour = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "NEMOURIDAE"]
, na.rm = TRUE)
, nt_NonIns = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (CLASS != "INSECTA"
| is.na(CLASS))]
, na.rm = TRUE)
, nt_Nudib = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "NUDIBRANCHIA"]
, na.rm = TRUE)
, nt_Odon = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ODONATA"]
, na.rm = TRUE)
, nt_OET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")]
, na.rm = TRUE)
, nt_Oligo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA")]
, na.rm = TRUE)
, nt_Perlid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "PERLIDAE"]
, na.rm = TRUE)
, nt_Pleco = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "PLECOPTERA"]
, na.rm = TRUE)
, nt_POET = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")]
, na.rm = TRUE)
, nt_POETNoBae = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "PLECOPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "ODONATA")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")]
, na.rm = TRUE)
, nfam_Baetidae = dplyr::n_distinct(FAMILY[EXCLUDE != TRUE
& FAMILY == "BAETIDAE"]
, na.rm = TRUE)
, nt_POETfamBae = nt_POETNoBae + nfam_Baetidae
, nt_Poly = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "POLYCHAETA"]
, na.rm = TRUE)
, nt_PolyNoSpion = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& CLASS == "POLYCHAETA"
& (is.na(FAMILY) == TRUE
| FAMILY != "SPIONIDAE")]
, na.rm = TRUE)
, nt_Ptero = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GENUS == "PTERONARCYS"]
, na.rm = TRUE)
, nt_Rhya = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GENUS == "RHYACOPHILA"]
, na.rm = TRUE)
, nt_Spion = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "SPIONIDAE"]
, na.rm = TRUE)
, nt_Tipulid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "TIPULIDAE"]
, na.rm = TRUE)
, nt_Trich = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
, nt_TrichNoHydro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE")]
, na.rm = TRUE)
, nt_Tromb = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TROMBIDIFORMES"]
, na.rm = TRUE)
, nt_Tubif = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "TUBIFICIDAE"]
, na.rm = TRUE)
# ,intolMol, ,
#### pi_phylo ####
, pi_Ampe = NA #pi_Ampeliscidae
, pi_AmpeHaust = NA
, pi_Amph = 100 * sum(N_TAXA[ORDER == "AMPHIPODA"]
, na.rm = TRUE) / ni_total
, pi_AmphIsop = 100 * sum(N_TAXA[ORDER == "AMPHIPODA"
| ORDER == "ISOPODA"]
, na.rm = TRUE) / ni_total
, pi_Baet = 100 * sum(N_TAXA[FAMILY == "BAETIDAE"]
, na.rm = TRUE) / ni_total
#, pi_Baet2Ephem
, pi_Bival = 100 * sum(N_TAXA[CLASS == "BIVALVIA"]
, na.rm = TRUE) / ni_total
, pi_Caen = 100 * sum(N_TAXA[FAMILY == "CAENIDAE"]
, na.rm = TRUE) / ni_total
, pi_Capit = 100 * sum(N_TAXA[FAMILY == "CAPITELLIDAE"]
, na.rm = TRUE) / ni_total
, pi_Cheu = 100 * sum(N_TAXA[GENUS == "CHEUMATOPSYCHE"]
, na.rm = TRUE) / ni_total
, pi_CheuSimHyalella = 100 * sum(N_TAXA[GENUS == "CHEUMATOPSYCHE"
| GENUS == "SIMULIUM"
| GENUS == "HYALELLA"]
, na.rm = TRUE) / ni_total
, pi_Cirra = 100 * sum(N_TAXA[FAMILY == "CIRRATULIDAE"]
, na.rm = TRUE) / ni_total
, pi_Clite = 100 * sum(N_TAXA[CLASS == "CLITELLATA"]
, na.rm = TRUE) / ni_total
, pi_Coleo = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"]
, na.rm = TRUE) / ni_total
, pi_COET = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Corb = 100 * sum(N_TAXA[GENUS == "CORBICULA"]
, na.rm = TRUE) / ni_total
, pi_CorixPhys = 100 * sum(N_TAXA[FAMILY == "CORIXIDAE"
| FAMILY == "PHYSIDAE"]
, na.rm = TRUE) / ni_total
, pi_CraCaeGam = 100 * sum(N_TAXA[GENUS == "CRANGONYX"
| GENUS == "CAECIDOTEA"
| GENUS == "GAMMARUS"]
, na.rm = TRUE) / ni_total
, pi_Cru = 100 * sum(N_TAXA[SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE) / ni_total
, pi_CruMol = 100 * sum(N_TAXA[PHYLUM == "MOLLUSCA"
| SUBPHYLUM == "CRUSTACEA"]
, na.rm = TRUE) / ni_total
, pi_Deca = 100 * sum(N_TAXA[ORDER == "DECAPODA"]
, na.rm = TRUE) / ni_total
, pi_Dipt = 100 * sum(N_TAXA[ORDER == "DIPTERA"]
, na.rm = TRUE) / ni_total
, pi_DiptNonIns = 100 * sum(N_TAXA[ORDER == "DIPTERA"
| CLASS != "INSECTA"
| is.na(CLASS)]
, na.rm = TRUE) / ni_total
, pi_ECT = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "COLEOPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Ephem = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE) / ni_total
, pi_EphemNoCae = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "CAENIDAE")]
, na.rm = TRUE) / ni_total
, pi_EphemNoCaeBae = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "CAENIDAE")
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")]
, na.rm = TRUE) / ni_total
, pi_EphemNoBaeTri = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE")
& (is.na(GENUS) == TRUE
| GENUS != "TRICORYTHODES")]
, na.rm = TRUE) / ni_total
, pi_EPT = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_EPTNoBaeHydro = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "BAETIDAE"))
| (ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE"))
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_EPTNoCheu = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA"
& (is.na(GENUS) == TRUE
| GENUS != "CHEUMATOPSYCHE")]
, na.rm = TRUE) / ni_total
, pi_EPTNoHydro = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA")
| (ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE
| FAMILY != "HYDROPSYCHIDAE"))
| ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_ET = 100 * sum(N_TAXA[ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Gast = 100 * sum(N_TAXA[CLASS == "GASTROPODA"]
, na.rm = TRUE) / ni_total
, pi_Haust = 100 * sum(N_TAXA[FAMILY == "HAUSTORIIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hemipt = 100 * sum(N_TAXA[ORDER == "HEMIPTERA"]
, na.rm = TRUE) / ni_total
, pi_Hesion = 100 * sum(N_TAXA[FAMILY == "HESIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hydro = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE) / ni_total
, pi_Hydro2EPT = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE)/ni_EPT
, pi_Hydro2Trich = 100 * sum(N_TAXA[FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE)/ni_Trich
, pi_Insect = 100 * sum(N_TAXA[CLASS == "INSECTA"]
, na.rm = TRUE) / ni_total
, pi_Isop = 100 * sum(N_TAXA[ORDER == "ISOPODA"]
, na.rm = TRUE) / ni_total
, pi_IsopGastHiru = 100 * sum(N_TAXA[ORDER == "ISOPODA"
| CLASS == "GASTROPODA"
| SUBCLASS == "HIRUDINEA"]
, na.rm = TRUE) / ni_total
, pi_Juga = 100 * sum(N_TAXA[GENUS == "JUGA"]
, na.rm = TRUE) / ni_total
, pi_JugaFlumi = 100 * sum(N_TAXA[GENUS == "JUGA"
| GENUS == "FLUMINICOLA"]
, na.rm = TRUE) / ni_total
, pi_Lucin = 100 * sum(N_TAXA[FAMILY == "LUCINIDAE"]
, na.rm = TRUE) / ni_total
, pi_LucinTellin = 100 * sum(N_TAXA[FAMILY == "LUCINIDAE"
| FAMILY == "TELLINIDAE"]
, na.rm = TRUE) / ni_total
, pi_Mega = 100 * sum(N_TAXA[ORDER == "MEGALOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Mol = 100 * sum(N_TAXA[PHYLUM == "MOLLUSCA"]
, na.rm = TRUE) / ni_total
, pi_Nemata = 100 * sum(N_TAXA[PHYLUM == "NEMATA"]
, na.rm = TRUE) / ni_total
, pi_Nereid = 100 * sum(N_TAXA[FAMILY == "NEREIDIDAE"]
, na.rm = TRUE) / ni_total
, pi_Nudib = 100 * sum(N_TAXA[ORDER == "NUDIBRANCHIA"]
, na.rm = TRUE) / ni_total
, pi_NonIns = 100 * sum(N_TAXA[CLASS != "INSECTA"
| is.na(CLASS)]
, na.rm = TRUE) / ni_total
, pi_Odon = 100 * sum(N_TAXA[ORDER == "ODONATA"]
, na.rm = TRUE) / ni_total
, pi_OET = 100 * sum(N_TAXA[ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Oligo = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"]
, na.rm = TRUE) / ni_total
, pi_OligoChiroHydro = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"
| FAMILY == "CHIRONOMIDAE"
| FAMILY == "HYDROPSYCHIDAE"]
, na.rm = TRUE) / ni_total
, pi_OligoHiru = 100 * sum(N_TAXA[CLASS == "OLIGOCHAETA"
| SUBCLASS == "OLIGOCHAETA"
| SUBCLASS == "HIRUDINEA"]
, na.rm = TRUE) / ni_total
, pi_Orbin = 100 * sum(N_TAXA[FAMILY == "ORBINIIDAE"]
, na.rm = TRUE) / ni_total
, pi_Pleco = 100 * sum(N_TAXA[ORDER == "PLECOPTERA"]
, na.rm = TRUE) / ni_total
, pi_POET = 100 * sum(N_TAXA[ORDER == "PLECOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_Poly = 100 * sum(N_TAXA[CLASS == "POLYCHAETA"]
, na.rm = TRUE) / ni_total
, pi_Spion = 100 * sum(N_TAXA[FAMILY == "SPIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Spion2Poly = 100 * sum(N_TAXA[CLASS == "POLYCHAETA" |
FAMILY == "SPIONIDAE"]
, na.rm = TRUE) / ni_total
, pi_Sphaer = 100 * sum(N_TAXA[FAMILY == "SPHAERIIDAE"]
, na.rm = TRUE) / ni_total
, pi_SphaerCorb = 100 * sum(N_TAXA[FAMILY == "SPHAERIIDAE" |
GENUS == "CORBICULA"]
, na.rm = TRUE) / ni_total
, pi_Tellin = 100 * sum(N_TAXA[FAMILY == "TELLINIDAE"]
, na.rm = TRUE) / ni_total
, pi_Trich = 100 * sum(N_TAXA[ORDER == "TRICHOPTERA"]
, na.rm = TRUE) / ni_total
, pi_TrichNoHydro = 100 * sum(N_TAXA[ORDER == "TRICHOPTERA"
& (is.na(FAMILY) == TRUE |
FAMILY != "HYDROPSYCHIDAE")]
, na.rm = TRUE) / ni_total
, pi_Tromb = 100 * sum(N_TAXA[ORDER == "TROMBIDIFORMES"]
, na.rm = TRUE) / ni_total
, pi_Tubif = 100 * sum(N_TAXA[FAMILY == "TUBIFICIDAE"]
, na.rm = TRUE) / ni_total
, pi_Xanth = 100 * sum(N_TAXA[FAMILY == "XANTHIDAE"]
, na.rm = TRUE) / ni_total
# Cole2Odon,
#EPTsenstive in tolerance group
#### pt_phylo ####
, pt_Amph = 100 * nt_Amph / nt_total
, pt_Bival = 100 * nt_Bival / nt_total
, pt_Coleo = 100 * nt_Coleo / nt_total
, pt_COET = 100 * nt_COET / nt_total
, pt_Deca = 100 * nt_Deca / nt_total
, pt_Dipt = 100 * nt_Dipt / nt_total
, pt_ECT = 100 * nt_ECT / nt_total
, pt_Ephem = 100 * nt_Ephem / nt_total
, pt_EPT = 100 * nt_EPT / nt_total
, pt_ET = 100 * nt_ET / nt_total
, pt_Gast = 100 * nt_Gast / nt_total
, pt_Hemipt = 100 * nt_Hemipt / nt_total
, pt_Insect = 100 * nt_Insect / nt_total
, pt_Isop = 100 * nt_Isop / nt_total
, pt_Mega = 100 * nt_Mega / nt_total
, pt_NonIns = 100 * nt_NonIns / nt_total
, pt_Nudib = 100 * nt_Nudib / nt_total
, pt_Odon = 100 * nt_Odon / nt_total
, pt_OET = 100 * nt_OET / nt_total
, pt_Oligo = 100 * nt_Oligo / nt_total
, pt_Pleco = 100 * nt_Pleco / nt_total
, pt_POET = 100 * nt_POET / nt_total
, pt_Poly = 100 * nt_Poly / nt_total
, pt_PolyNoSpion = 100 * nt_PolyNoSpion / nt_total
, pt_Spion = 100 * nt_Spion / nt_total
, pt_Trich = 100 * nt_Trich / nt_total
, pt_TrichNoHydro = 100 * nt_TrichNoHydro / nt_total
, pt_Tromb = 100 * nt_Tromb / nt_total
#### ratio_phylo ####
# nt_X / log(ni_total)
# X = specialty group, e.g., Bivalves
# Log is natural log
#, rt_Amph = nt_Amph
#, rt_AmpCar = nt_AmpCar
#, rt_Bivalve = nt_Bivalve
#, rt_Capit = nt_Capit
#, rt_Car = nt_Car
#, rt_Coleo = nt_Coleo
#, rt_CruMol = nt_CruMol
#, rt_Deca = nt_Deca
#, rt_Ephem = nt_Ephem
#, rt_EPT = nt_EPT
#, rt_Gast = nt_Gast
#, rt_Isop = nt_Isop
#, rt_Nereid = nt_Nereid
#, rt_Nudib = nt_Nudib
#, rt_Oligo = nt_Oligo
#, rt_Pleco = nt_Pleco
#, rt_Poly = nt_Poly
#, rt_PolyNoSpion = nt_PolyNoSpion
#, rt_Ptero = nt_Ptero
#, rt_Spion = nt_Spion
#, rt_Trich = nt_Trich
#, rt_Tubif = nt_Tubif
### Midges ####
# Family = Chironomidae
# subfamily = Chironominae
# subfamily = Orthocladiinae
# subfamily = Tanypodinae
# Tribe = Tanytarsini
, nt_Chiro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CHIRONOMIDAE"]
, na.rm = TRUE)
, pi_Chiro = 100 * ni_Chiro / ni_total
, pt_Chiro = 100 * nt_Chiro / nt_total
, pi_Ortho = 100 * sum(N_TAXA[SUBFAMILY == "ORTHOCLADIINAE"]
, na.rm = TRUE) / ni_total
, pi_Tanyt = 100 * sum(N_TAXA[TRIBE == "TANYTARSINI"]
, na.rm = TRUE) / ni_total
, pi_Tanyp = 100 * sum(N_TAXA[SUBFAMILY == "TANYPODINAE"]
, na.rm = TRUE) / ni_total
, pi_Chi2Dipt = 100 * ni_Chiro / ni_Dipt
, pi_COC2Chi = 100 * sum(N_TAXA[GENUS == "CHIRONOMUS"
| GENUS == "CRICOTOPUS"
| GENUS == "CRICOTOPUS/ORTHOCLADIUS"
| GENUS == "ORTHOCLADIUS/CRICOTOPUS"
| GENUS == "ORTHOCLADIUS"]
, na.rm = TRUE)/ni_Chiro
, pi_ChCr2Chi = 100 * sum(N_TAXA[GENUS == "CHIRONOMUS"
| GENUS == "CRICOTOPUS"]
, na.rm = TRUE)/ni_Chiro
, pi_Orth2Chi = 100 * sum(N_TAXA[SUBFAMILY == "ORTHOCLADIINAE"]
, na.rm = TRUE)/ni_Chiro
, pi_Tanyp2Chi = 100 * sum(N_TAXA[SUBFAMILY == "TANYPODINAE"]
, na.rm = TRUE)/ni_Chiro
#,nt_Ortho (Marine)
#MB_pi_OrthocladiinaeCricotopusChironomus2Chironomidae
# rt_Chiro, Ortho, Tanyt
, pi_ChiroAnne = 100 * sum(N_TAXA[PHYLUM == "ANNELIDA"
| FAMILY == "CHIRONOMIDAE"]
, na.rm = TRUE) / ni_total
### Other misc ----
# dominant
, pi_dom02_BCG_att456_NoJugaRiss = 100 * max(ni_dom02_NoJugaRiss_BCG_att456) / ni_total
#
# 20180608, rework PacNW
# NonINSECTA, Attribute 456
, nt_NonIns_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonIns_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonIns_BCG_att456 = 100 * nt_NonIns_BCG_att456 / nt_total
# NonInsectaJugaRiss, Attribute 456
, nt_NonInsJugaRiss_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "RISSOOIDEA")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsJugaRiss_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "RISSOOIDEA")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsJugaRiss_BCG_att456 = 100 * nt_NonInsJugaRiss_BCG_att456 / nt_total
# 20180815, Percent BAETIS TRICAUDATUS COMPLEX + SIMULIIDAE individual
, pi_SimBtri = 100 * (sum(N_TAXA[FAMILY == "SIMULIIDAE"], na.rm = TRUE)
+ sum(N_TAXA[TAXAID == "BAETIS TRICAUDATUS COMPLEX"]
, na.rm = TRUE)) / ni_total
# 20181018, MS, sensitive COLEOPTERA & (Family is Null or not Hydrophyilidae)
, pi_Colesens = 100 * sum(N_TAXA[ORDER == "COLEOPTERA"
& (FAMILY != "HYDROPHILIDAE"
| is.na(FAMILY) == TRUE)]
, na.rm = TRUE) / ni_total
# 20181207, BCG PacNW, Level 1 Signal metrics
, nt_longlived = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LONGLIVED == TRUE]
, na.rm = TRUE)
, pt_longlived = 100 * nt_longlived / nt_total
, nt_noteworthy = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NOTEWORTHY == TRUE]
, na.rm = TRUE)
, nt_ffg2_pred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG2_PRE == TRUE]
, na.rm = TRUE)
, ni_Noto = sum(N_TAXA[GENUS == "NOTOMASTUS"], na.rm = TRUE)
### Thermal Indicators ----
#### nt_ti----
, nt_ti_stenocold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_STENOCOLD == TRUE]
, na.rm = TRUE)
, nt_ti_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COLD == TRUE]
, na.rm = TRUE)
, nt_ti_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COOL == TRUE]
, na.rm = TRUE)
, nt_ti_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_WARM == TRUE]
, na.rm = TRUE)
, nt_ti_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_STENOWARM == TRUE]
, na.rm = TRUE)
, nt_ti_eury = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_EURY == TRUE]
, na.rm = TRUE)
, nt_ti_cowa = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COWA == TRUE]
, na.rm = TRUE)
, nt_ti_na = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_NA == TRUE]
, na.rm = TRUE)
, nt_ti_stenocold_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_STENOCOLD == TRUE |
TI_COLD == TRUE)]
, na.rm = TRUE)
, nt_ti_stenocold_cold_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_STENOCOLD == TRUE |
TI_COLD == TRUE |
TI_COOL == TRUE)]
, na.rm = TRUE)
, nt_ti_cowa_warm_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_COWA == TRUE |
TI_WARM == TRUE |
TI_STENOWARM == TRUE )]
, na.rm = TRUE)
, nt_ti_warm_stenowarm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_WARM == TRUE |
TI_STENOWARM == TRUE)]
, na.rm = TRUE)
#### pi_ti----
, pi_ti_stenocold = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cold = 100 * sum(N_TAXA[TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool = 100 * sum(N_TAXA[TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm = 100 * sum(N_TAXA[TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenowarm = 100 * sum(N_TAXA[TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_eury = 100 * sum(N_TAXA[TI_EURY == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cowa = 100 * sum(N_TAXA[TI_COWA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_na = 100 * sum(N_TAXA[TI_NA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenocold_cold = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE |
TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_stenocold_cold_cool = 100 * sum(N_TAXA[TI_STENOCOLD == TRUE |
TI_COLD == TRUE |
TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cowa_warm_stenowarm = 100 * sum(N_TAXA[TI_COWA == TRUE |
TI_WARM == TRUE |
TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm_stenowarm = 100 * sum(N_TAXA[TI_WARM == TRUE |
TI_STENOWARM == TRUE]
, na.rm = TRUE) / ni_total
#### pt_ti ----
, pt_ti_stenocold = 100 * nt_ti_stenocold / nt_total
, pt_ti_cold = 100 * nt_ti_cold / nt_total
, pt_ti_cool = 100 * nt_ti_cool / nt_total
, pt_ti_warm = 100 * nt_ti_warm / nt_total
, pt_ti_stenowarm = 100 * nt_ti_stenowarm / nt_total
, pt_ti_eury = 100 * nt_ti_eury / nt_total
, pt_ti_cowa = 100 * nt_ti_cowa / nt_total
, pt_ti_na = 100 * nt_ti_na / nt_total
, pt_ti_stenocold_cold = 100 * nt_ti_stenocold_cold / nt_total
, pt_ti_stenocold_cold_cool = 100 * nt_ti_stenocold_cold_cool / nt_total
, pt_ti_cowa_warm_stenowarm = 100 * nt_ti_cowa_warm_stenowarm / nt_total
, pt_ti_warm_stenowarm = 100 * nt_ti_warm_stenowarm / nt_total
### ratio
, ri_ti_sccc_wsw = pi_ti_stenocold_cold_cool / pi_ti_warm_stenowarm
### Tolerance ----
# 4 and 6 are WV GLIMPSS (no equal)
, nt_tv_intol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 3]
, na.rm = TRUE)
, nt_tv_intol2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 2]
, na.rm = TRUE)
, nt_tv_intol4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL < 4]
, na.rm = TRUE)
, nt_tv_toler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 7
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_tv_toler6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 6
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_tv_toler8 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE)
, pi_tv_intol = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL <= 3], na.rm = TRUE) / ni_total
, pi_tv_intol4 = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL < 4], na.rm = TRUE) / ni_total
, pi_tv_toler = 100 * sum(N_TAXA[TOLVAL >= 7
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pi_tv_toler6 = 100 * sum(N_TAXA[TOLVAL > 6
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pi_tv_toler8 = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10], na.rm = TRUE) / ni_total
, pt_tv_intol = 100 * nt_tv_intol / nt_total
, pt_tv_intol4 = 100 * nt_tv_intol4 / nt_total
, pt_tv_toler = 100 * nt_tv_toler / nt_total
, pt_tv_toler6 = 100 * nt_tv_toler6 / nt_total
, pt_tv_toler8 = 100 * nt_tv_toler8 / nt_total
#,nt_tvfam_intol = dplyr::n_distinct(TAXAID[EXCLUDE!=TRUE & FAM_TV<=3 & !is.na(FAM_TV)])
# pi_Baet2Eph, pi_Hyd2EPT, pi_Hyd2Tri, in Pct Ind group
# nt_intMol (for marine)
# intol4_EPT is PA not WV so [0-4].
, nt_tv_intol4_EPT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 4
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")]
, na.rm = TRUE)
# USEPA, WSA and NRSA
## ntol is not tolerant
## stol is super tolerant
, nt_tv_ntol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL < 6]
, na.rm = TRUE)
, nt_tv_stol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE)
, pi_tv_ntol = 100 * sum(N_TAXA[TOLVAL >= 0
& TOLVAL < 6]
, na.rm = TRUE) / ni_total
, pi_tv_stol = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE) / ni_total
, pt_tv_ntol = 100 * nt_tv_ntol / nt_total
, pt_tv_stol = 100 * nt_tv_stol / nt_total
### Tolerance2 ####
## special condition tolerance values
# MBSS
, pi_tv2_intol = sum(N_TAXA[TOLVAL2 <= 3
& !is.na(TOLVAL2)])/sum(N_TAXA[!is.na(TOLVAL2)])
#, pi_tv_intolurb=pi_tv2_intol
, pi_tv2_toler_ISA_SalHi_xFL = NA
, pi_tv2_intol_ISA_SalHi_xFL = NA
, pt_tv2_intol_ISA_SalHi_xFL = NA
### FFG #####
#### nt_ffg----
, nt_ffg_col = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_COL == TRUE]
, na.rm = TRUE)
, nt_ffg_filt = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_FIL == TRUE]
, na.rm = TRUE)
, nt_ffg_pred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PRE == TRUE]
, na.rm = TRUE)
, nt_ffg_scrap = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_SCR == TRUE]
, na.rm = TRUE)
, nt_ffg_shred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_SHR == TRUE]
, na.rm = TRUE)
, nt_ffg_mah = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_MAH == TRUE]
, na.rm = TRUE)
, nt_ffg_omn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_OMN == TRUE]
, na.rm = TRUE)
, nt_ffg_par = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PAR == TRUE]
, na.rm = TRUE)
, nt_ffg_pih = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PIH == TRUE]
, na.rm = TRUE)
, nt_ffg_xyl = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_XYL == TRUE]
, na.rm = TRUE)
, nt_ffg_pred_scrap_shred = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (FFG_PRE == TRUE |
FFG_SCR == TRUE |
FFG_SHR == TRUE)]
, na.rm = TRUE)
, nt_ffg_pred_NoChi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FFG_PRE == TRUE
& (is.na(FAMILY) == TRUE
| FAMILY != "CHIRONOMIDAE")]
, na.rm = TRUE)
#### pi_ffg----
, pi_ffg_col = 100 * sum(N_TAXA[FFG_COL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_filt = 100 * sum(N_TAXA[FFG_FIL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_pred = 100 * sum(N_TAXA[FFG_PRE == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_scrap = 100 * sum(N_TAXA[FFG_SCR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_shred = 100 * sum(N_TAXA[FFG_SHR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_mah = 100 * sum(N_TAXA[FFG_MAH == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_omn = 100 * sum(N_TAXA[FFG_OMN == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_par = 100 * sum(N_TAXA[FFG_PAR == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_pih = 100 * sum(N_TAXA[FFG_PIH == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_xyl = 100 * sum(N_TAXA[FFG_XYL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ffg_col_filt = 100 * sum(N_TAXA[FFG_COL == TRUE |
FFG_FIL == TRUE]
, na.rm = TRUE) / ni_total
#### pt_ffg----
, pt_ffg_col = 100 * nt_ffg_col / nt_total
, pt_ffg_filt = 100 * nt_ffg_filt / nt_total
, pt_ffg_pred = 100 * nt_ffg_pred / nt_total
, pt_ffg_scrap = 100 * nt_ffg_scrap / nt_total
, pt_ffg_shred = 100 * nt_ffg_shred / nt_total
, pt_ffg_mah = 100 * nt_ffg_mah / nt_total
, pt_ffg_omn = 100 * nt_ffg_omn / nt_total
, pt_ffg_par = 100 * nt_ffg_par / nt_total
, pt_ffg_pih = 100 * nt_ffg_pih / nt_total
, pt_ffg_xyl = 100 * nt_ffg_xyl / nt_total
#, pi_ffg_infc
#, rt_ffg_infc, converborbelt, scavbrow, subsurf, watercol
#, rt_ffg_pred
# carnivoreomnivore, deepdeposit, suspension
### FFG2 ####
# marine
## nt_ffg2
, nt_ffg2_intface = NA
, nt_ffg2_subsurf = NA
## pi_ffg2
, pi_ffg2_scavburr = NA
## pt_ffg2
# = conveyorbelt, interface, scavengerbrowser, subsurface, watercolumn, predator
### Habit ####
#(need to be wild card. that is, counts both CN,CB and CB as climber)
#### nt_habit----
, nt_habit_burrow = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_BU == TRUE]
, na.rm = TRUE)
, nt_habit_climb = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_CB == TRUE]
, na.rm = TRUE)
, nt_habit_climbcling = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (HABIT_CB == TRUE
| HABIT_CN == TRUE)])
, nt_habit_cling = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_CN == TRUE]
, na.rm = TRUE)
, nt_habit_skate = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SK == TRUE]
, na.rm = TRUE)
, nt_habit_sprawl = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SP == TRUE]
, na.rm = TRUE)
, nt_habit_swim = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABIT_SW == TRUE]
, na.rm = TRUE)
#### pi_habit----
, pi_habit_burrow = 100 * sum(N_TAXA[HABIT_BU == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_climb = 100 * sum(N_TAXA[HABIT_CB == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_climbcling = 100 * sum(N_TAXA[HABIT_CB == TRUE
| HABIT_CN == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_cling = 100 * sum(N_TAXA[HABIT_CN == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_skate = 100 * sum(N_TAXA[HABIT_SK == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_sprawl = 100 * sum(N_TAXA[HABIT_SP == TRUE]
, na.rm = TRUE) / ni_total
, pi_habit_swim = 100 * sum(N_TAXA[HABIT_SW == TRUE]
, na.rm = TRUE) / ni_total
#### pt_habit----
, pt_habit_burrow = 100 * nt_habit_burrow / nt_total
, pt_habit_climb = 100 * nt_habit_climb / nt_total
, pt_habit_climbcling = 100 * nt_habit_climbcling / nt_total
, pt_habit_cling = 100 * nt_habit_cling / nt_total
, pt_habit_skate = 100 * nt_habit_sprawl / nt_total
, pt_habit_sprawl = 100 * nt_habit_sprawl / nt_total
, pt_habit_swim = 100 * nt_habit_swim / nt_total
## Oddball
# might not need habit != cling for Pleco
, pi_habit_cling_PlecoNoCling = 100 * sum(N_TAXA[HABIT_CN == TRUE
| (ORDER == "PLECOPTERA"
& HABIT_CN == FALSE)]
, na.rm = TRUE) / ni_total
### Life Cycle ####
# pi and nt for mltvol, semvol, univol
#### nt_LifeCycle----
, nt_volt_multi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_MULTI == TRUE]
, na.rm = TRUE)
, nt_volt_semi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_SEMI == TRUE]
, na.rm = TRUE)
, nt_volt_uni = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LC_UNI == TRUE]
, na.rm = TRUE)
#### pi_LifeCycle----
, pi_volt_multi = 100 * sum(N_TAXA[LC_MULTI == TRUE]
, na.rm = TRUE) / ni_total
, pi_volt_semi = 100 * sum(N_TAXA[LC_SEMI == TRUE]
, na.rm = TRUE) / ni_total
, pi_volt_uni = 100 * sum(N_TAXA[LC_UNI == TRUE]
, na.rm = TRUE) / ni_total
#### pt_LifeCycle----
, pt_volt_multi = 100 * nt_volt_multi / nt_total
, pt_volt_semi = 100 * nt_volt_semi / nt_total
, pt_volt_uni = 100 * nt_volt_uni / nt_total
### Dominant N ####
## uses previously defined values added to myDF
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
, pi_dom03 = 100 * max(ni_dom03, na.rm = TRUE) / ni_total
, pi_dom04 = 100 * max(ni_dom04, na.rm = TRUE) / ni_total
, pi_dom05 = 100 * max(ni_dom05, na.rm = TRUE) / ni_total
, pi_dom06 = 100 * max(ni_dom06, na.rm = TRUE) / ni_total
, pi_dom07 = 100 * max(ni_dom07, na.rm = TRUE) / ni_total
, pi_dom08 = 100 * max(ni_dom08, na.rm = TRUE) / ni_total
, pi_dom09 = 100 * max(ni_dom09, na.rm = TRUE) / ni_total
, pi_dom10 = 100 * max(ni_dom10, na.rm = TRUE) / ni_total
# , pi_dom01alt= dplyr::top_n(N_TAXA, n=1) / ni_total
#https://stackoverflow.com/questions/27766054/getting-the-top-values-by-group
# top_n uses ties so can't use it
### Indices ####
#, x_AMBI - may need extra function or like "top" functions do some precalc
#,x_Becks.CLASS1=n_distinct(N_TAXA[EXCLUDE!=TRUE & TolVal>=0 & TolVal<=2.5])
#,x_Becks.CLASS2=n_distinct(N_TAXA[EXCLUDE!=TRUE & TolVal>=2.5 & TolVal<=4])
, x_Becks = (2 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 1.5]
, na.rm = TRUE)) +
(1 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 1.5
& TOLVAL <= 4]
, na.rm = TRUE))
, x_Becks3 = (3 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 0
& TOLVAL <= 0.5]
, na.rm = TRUE)) +
(2 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 0.5
& TOLVAL <= 1.5]
, na.rm = TRUE)) +
(1 * dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL > 1.5
& TOLVAL <= 2.5]
, na.rm = TRUE))
#,x_HBI_numer=sum(N_TAXA*TOLVAL, na.rm = TRUE)
#,x_HBI_denom=sum(N_TAXA[!is.na(TOLVAL) & TOLVAL>=0], na.rm = TRUE)
, x_HBI = sum(N_TAXA * TOLVAL, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL)
& TOLVAL >= 0]
, na.rm = TRUE)
, x_HBI2 = sum(N_TAXA * TOLVAL2, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL2)
& TOLVAL2 >= 0]
, na.rm = TRUE)
, x_NCBI = sum(N_TAXA * TOLVAL2, na.rm = TRUE)/sum(N_TAXA[!is.na(TOLVAL2)
& TOLVAL2 >= 0]
, na.rm = TRUE)
, x_BCICTQa = sum(TOLVAL2[EXCLUDE != TRUE], na.rm = TRUE) / nt_total
# Shannon-Weiner
#, x_Shan_Num= -sum(log(N_TAXA / ni_total)), na.rm = TRUE)
#, x_Shan_e=x_Shan_Num/log(exp(1))
, x_Shan_e = -sum((N_TAXA / ni_total) * log((N_TAXA / ni_total))
, na.rm = TRUE)
, x_Shan_2 = x_Shan_e/log(2)
, x_Shan_10 = x_Shan_e/log(10)
#, x_D Simpson
, x_D = 1 - sum((N_TAXA / ni_total)^2, na.rm = TRUE)
#, X_D_G (Gleason) - [nt_total]/Log([ni_total])
, x_D_G = (nt_total) / log(ni_total)
#, x_D_Mg Margalef - ([nt_total]-1)/Log([ni_total])
, x_D_Mg = (nt_total - 1) / log(ni_total)
#, x_Hbe
#, x_H (Shannon)
# Evenness, Pielou
# H / Hmax Hmax is log(nt_total)
, x_Evenness = x_Shan_e/log(nt_total)
# evenness - different from Pielou in MS Coastal Metric Calc 2011 db
### Density ####
# Numbers per area sampled
### Estuary-Marine ####
# Mixed in with other metrics
, x_Becks_tv2 = NA
### Habitat ####
# BCG PacNW group 2020
# BRAC brackish
# DEPO depositional
# GENE generalist
# HEAD headwater
# RHEO rheophily
# RIVE riverine
# SPEC specialist
# UNKN unknown
#
#### nt_habitat----
, nt_habitat_brac = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_BRAC == TRUE]
, na.rm = TRUE)
, nt_habitat_depo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_DEPO == TRUE]
, na.rm = TRUE)
, nt_habitat_gene = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_GENE == TRUE]
, na.rm = TRUE)
, nt_habitat_head = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_HEAD == TRUE]
, na.rm = TRUE)
, nt_habitat_lent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_LENT == TRUE]
, na.rm = TRUE)
, nt_habitat_loti = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_LOTI == TRUE]
, na.rm = TRUE)
, nt_habitat_rheo = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_RHEO == TRUE]
, na.rm = TRUE)
, nt_habitat_rive = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_RIVE == TRUE]
, na.rm = TRUE)
, nt_habitat_spec = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_SPEC == TRUE]
, na.rm = TRUE)
, nt_habitat_terr = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_TERR == TRUE]
, na.rm = TRUE)
, nt_habitat_unkn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_UNKN == TRUE]
, na.rm = TRUE)
#### pi_habitat----
, pi_habitat_brac = 100 * sum(N_TAXA[HABITAT_BRAC == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_depo = 100 * sum(N_TAXA[HABITAT_DEPO == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_gene = 100 * sum(N_TAXA[HABITAT_GENE == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_head = 100 * sum(N_TAXA[HABITAT_HEAD == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_lent = 100 * sum(N_TAXA[HABITAT_LENT == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_loti = 100 * sum(N_TAXA[HABITAT_LOTI == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_rheo = 100 * sum(N_TAXA[HABITAT_RHEO == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_rive = 100 * sum(N_TAXA[HABITAT_RIVE == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_spec = 100 * sum(N_TAXA[HABITAT_SPEC == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_terr = 100 * sum(N_TAXA[HABITAT_TERR == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_unkn = 100 * sum(N_TAXA[HABITAT_UNKN == TRUE]
, na.rm = TRUE) / ni_total
#### pt_habitat----
, pt_habitat_brac = 100 * nt_habitat_brac / nt_total
, pt_habitat_depo = 100 * nt_habitat_depo / nt_total
, pt_habitat_gene = 100 * nt_habitat_gene / nt_total
, pt_habitat_head = 100 * nt_habitat_head / nt_total
, pt_habitat_lent = 100 * nt_habitat_lent / nt_total
, pt_habitat_loti = 100 * nt_habitat_loti / nt_total
, pt_habitat_rheo = 100 * nt_habitat_rheo / nt_total
, pt_habitat_rive = 100 * nt_habitat_rive / nt_total
, pt_habitat_spec = 100 * nt_habitat_spec / nt_total
, pt_habitat_terr = 100 * nt_habitat_terr / nt_total
, pt_habitat_unkn = 100 * nt_habitat_unkn / nt_total
### BCG ####
# 1i, 1m, 1t
# Xi, Xm, Xt
# 5i, 5m, 5t
# 6i, 6m, 6t
# toupper(), 2022-02-22
#### BCG_nt----
, nt_BCG_att1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1"]
, na.rm = TRUE)
, nt_BCG_att1i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1I"]
, na.rm = TRUE)
, nt_BCG_att1m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1M"]
, na.rm = TRUE)
, nt_BCG_att12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
&
(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1i23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1i236i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att45 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att56 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att56t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_att6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att6i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att6m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6M")]
, na.rm = TRUE)
, nt_BCG_att6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_attNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(BCG_ATTR)]
, na.rm = TRUE)
, nt_BCG_att4b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_BCG_att4w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE)
, nt_BCG_att1i234b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_BETTER"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att4w5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
#### BCG_nt_Phylo----
, nt_Ephem_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_EPT_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_EPT_BCG_att1i23 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_Pleco_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "PLECOPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_Trich_BCG_att1i2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_Coleo_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "COLEOPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Ephem_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "EPHEMEROPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Odon_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "ODONATA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_Trich_BCG_att234b4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ORDER == "TRICHOPTERA"
& (BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER"
| BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
#### BCG_pi----
, pi_BCG_att1 = 100 * sum(N_TAXA[(BCG_ATTR == "1")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i = 100 * sum(N_TAXA[(BCG_ATTR == "1I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1m = 100 * sum(N_TAXA[(BCG_ATTR == "1M")]
, na.rm = TRUE) / ni_total
, pi_BCG_att12 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i2 = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att123 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i23 = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i236i = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att2 = 100 * sum(N_TAXA[(BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att23 = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att234 = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG_att3 = 100 * sum(N_TAXA[(BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4 = 100 * sum(N_TAXA[(BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG_att45 = 100 * sum(N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att456 = 100 * sum(N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5 = 100 * sum(N_TAXA[(BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5extra = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "5.5")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56 = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56t = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6 = 100 * sum(N_TAXA[(BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6i = 100 * sum(N_TAXA[(BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6m = 100 * sum(N_TAXA[(BCG_ATTR == "6M")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6t = 100 * sum(N_TAXA[(BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_attNA = 100 * sum(N_TAXA[(is.na(BCG_ATTR) == TRUE)]
, na.rm = TRUE) / ni_total
, pi_BCG_att4b = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4m = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i234b = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_BETTER"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"]
, na.rm = TRUE)) / ni_total
, pi_BCG_att4w5 = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE)) / ni_total
#### BCG_pi_Phylo----
, pi_EPT_BCG_att123 = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_EPT_BCG_att1i23 = 100 * sum(N_TAXA[(ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"
| ORDER == "PLECOPTERA")
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
#### BCG_pt----
, pt_BCG_att1 = 100 * nt_BCG_att1 / nt_total
, pt_BCG_att1i = 100 * nt_BCG_att1i / nt_total
, pt_BCG_att1m = 100 * nt_BCG_att1m / nt_total
, pt_BCG_att12 = 100 * nt_BCG_att12 / nt_total
, pt_BCG_att1234 = 100 * nt_BCG_att1234 / nt_total
, pt_BCG_att1i2 = 100 * nt_BCG_att1i2 / nt_total
, pt_BCG_att123 = 100 * nt_BCG_att123 / nt_total
, pt_BCG_att1i23 = 100 * nt_BCG_att1i23 / nt_total
, pt_BCG_att1i236i = 100 * nt_BCG_att1i236i / nt_total
, pt_BCG_att2 = 100 * nt_BCG_att2 / nt_total
, pt_BCG_att23 = 100 * nt_BCG_att23 / nt_total
, pt_BCG_att234 = 100 * nt_BCG_att234 / nt_total
, pt_BCG_att3 = 100 * nt_BCG_att3 / nt_total
, pt_BCG_att4 = 100 * nt_BCG_att4 / nt_total
, pt_BCG_att45 = 100 * nt_BCG_att45 / nt_total
, pt_BCG_att456 = 100 * nt_BCG_att456 / nt_total
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
, pt_BCG_att56 = 100 * nt_BCG_att56 / nt_total
, pt_BCG_att56t = 100 * nt_BCG_att56t / nt_total
, pt_BCG_att6 = 100 * nt_BCG_att6 / nt_total
, pt_BCG_att6i = 100 * nt_BCG_att6i / nt_total
, pt_BCG_att6m = 100 * nt_BCG_att6m / nt_total
, pt_BCG_att6t = 100 * nt_BCG_att6t / nt_total
, pt_BCG_attNA = 100 * nt_BCG_attNA / nt_total
, pt_BCG_att4b = 100 * nt_BCG_att4b / nt_total
, pt_BCG_att4m = 100 * nt_BCG_att4m / nt_total
, pt_BCG_att4w = 100 * nt_BCG_att4w / nt_total
, pt_BCG_att1i234b = 100 * nt_BCG_att1i234b / nt_total
, pt_BCG_att4w5 = 100 * nt_BCG_att4w5 / nt_total
#### BCG_special ----
# BCG_pt_Phylo
, pt_EPT_BCG_att123 = 100 * nt_EPT_BCG_att123 / nt_total
, pt_EPT_BCG_att1i23 = 100 * nt_EPT_BCG_att1i23 / nt_total
#### BCG_pi_dom ----
, pi_dom01_BCG_att4 = 100 * max(0
, ni_dom01_BCG_att4
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5 = 100 * max(0
, ni_dom01_BCG_att5
, na.rm = TRUE) / ni_total
# domX_BCG
# pi_dom01_att 4, 5, 56
# pi_dom05_att 123, not 456
### UFC ----
#Taxonomic Uncertainty Frequency Class (use HBI calculation)
, x_UFC = sum(N_TAXA * UFC, na.rm = TRUE) / sum(N_TAXA[!is.na(UFC)
& UFC >= 1
& UFC <= 6]
, na.rm = TRUE)
### Elevation ----
, nt_elev_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ELEVATION_LOW == TRUE]
, na.rm = TRUE)
, nt_elev_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ELEVATION_HIGH == TRUE]
, na.rm = TRUE)
### Gradient ----
, nt_grad_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_LOW == TRUE]
, na.rm = TRUE)
, nt_grad_mod = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_MOD == TRUE]
, na.rm = TRUE)
, nt_grad_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& GRADIENT_HIGH == TRUE]
, na.rm = TRUE)
### WS_Area ----
, nt_wsarea_small = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_S == TRUE]
, na.rm = TRUE)
, nt_wsarea_medium = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_M == TRUE]
, na.rm = TRUE)
, nt_wsarea_large = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_L == TRUE]
, na.rm = TRUE)
, nt_wsarea_xlarge = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WSAREA_XL == TRUE]
, na.rm = TRUE)
### Habitat Structure ----
#### nt_habstruct----
, nt_habstruct_coarsesub = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_CS == TRUE]
, na.rm = TRUE)
, nt_habstruct_noflow = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_NF == TRUE]
, na.rm = TRUE)
, nt_habstruct_rootmat = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_RM == TRUE]
, na.rm = TRUE)
, nt_habstruct_snag = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HS_SG == TRUE]
, na.rm = TRUE)
, nt_habstruct_NA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(HABSTRUCT)]
, na.rm = TRUE)
#### pi_habstruct----
, pi_habstruct_coarsesub = 100 * sum(N_TAXA[HS_CS == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_noflow = 100 * sum(N_TAXA[HS_NF == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_rootmat = 100 * sum(N_TAXA[HS_RM == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_snag = 100 * sum(N_TAXA[HS_SG == TRUE]
, na.rm = TRUE) / ni_total
, pi_habstruct_NA = 100 * sum(N_TAXA[(is.na(HABSTRUCT) == TRUE)]
, na.rm = TRUE) / ni_total
#### pt_habstruct----
, pt_habstruct_coarsesub = 100 * nt_habstruct_coarsesub / nt_total
, pt_habstruct_noflow = 100 * nt_habstruct_noflow / nt_total
, pt_habstruct_rootmat = 100 * nt_habstruct_rootmat / nt_total
, pt_habstruct_snag = 100 * nt_habstruct_snag / nt_total
, pt_habstruct_NA = 100 * nt_habstruct_NA / nt_total
### nval_habstruct
, nval_habstruct = sum(HS_CS + HS_NF + HS_RM + HS_SG, na.rm = TRUE)
### Number Group within Group ----
#### nord_Order----
, nord_COET = dplyr::n_distinct(ORDER[ORDER == "COLEOPTERA"
| ORDER == "ODONATA"
| ORDER == "EPHEMEROPTERA"
| ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### nfam_Order----
, nfam_Coleo = dplyr::n_distinct(FAMILY[ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, nfam_Ephem = dplyr::n_distinct(FAMILY[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, nfam_Odon = dplyr::n_distinct(FAMILY[ORDER == "ODONATA"]
, na.rm = TRUE)
, nfam_Trich = dplyr::n_distinct(FAMILY[ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### ngen_Order----
, ngen_Coleo = dplyr::n_distinct(GENUS[ORDER == "COLEOPTERA"]
, na.rm = TRUE)
, ngen_Ephem = dplyr::n_distinct(GENUS[ORDER == "EPHEMEROPTERA"]
, na.rm = TRUE)
, ngen_Odon = dplyr::n_distinct(GENUS[ORDER == "ODONATA"]
, na.rm = TRUE)
, ngen_Trich = dplyr::n_distinct(GENUS[ORDER == "TRICHOPTERA"]
, na.rm = TRUE)
#### nfam_Family ----
# added next to nt_POET above for use with nt_POET_famBae
# so only code once
# , nfam_Baetidae = dplyr::n_distinct(FAMILY[EXCLUDE != TRUE
# & FAMILY == "BAETIDAE"]
# , na.rm = TRUE)
#### ngen_Family----
, ngen_Elmid = dplyr::n_distinct(GENUS[FAMILY == "ELMIDAE"]
, na.rm = TRUE)
### SPECIAL ####
# oddball or specialized metrics
# , ni_NonIns = sum(N_TAXA[CLASS==NA | CLASS!="INSECTA"], na.rm = TRUE)
# , ni_NonArach = sum(N_TAXA[CLASS==NA | CLASS!="ARACHNIDA"], na.rm = TRUE)
# , ni_NonDeca = sum(N_TAXA[ORDER==NA | ORDER!="DECAPODA"], na.rm = TRUE)
#
# , ni_clumpy = sum(N_TAXA[GENUS=="JUGA" & GENUS=="Rissoidea"], na.rm = TRUE)
# , ni_Nonclumpy = sum(N_TAXA[GENUS!="JUGA" & GENUS!="Rissoidea"], na.rm = TRUE)
#
# PacNW, NonIns_select
#This metric excludes Class INSECTA, Class ARACHNIDA and Order DECAPODA;
# and only includes Attribute IV, V, VI taxa.
, nt_NonInsArachDeca_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| ORDER != "DECAPODA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsArachDeca_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| ORDER != "DECAPODA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsArachDeca_BCG_att456 = 100 * nt_NonInsArachDeca_BCG_att456 / nt_total
# PacNW, NonIns_select_NonClump
# above but also non-clumpy
#clumpy' taxa (Juga [genus] and RISSOOIDEA [superfamily as Order] in PacNW);
#and it only includes Attribute IV, V, VI taxa.
, nt_NonInsArachDecaJugaRiss_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| (ORDER != "DECAPODA"
& ORDER != "RISSOOIDEA"))
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsArachDecaJugaRiss_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| (CLASS != "INSECTA"
& CLASS != "ARACHNIDA"))
& (is.na(ORDER) == TRUE
| (ORDER != "DECAPODA"
& ORDER != "RISSOOIDEA"))
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsArachDecaJugaRiss_BCG_att456 = 100 * nt_NonInsArachDecaJugaRiss_BCG_att456 / nt_total
, nt_NonInsTrombJuga_BCG_att456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "TROMBIDIFORMES")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, pi_NonInsTrombJuga_BCG_att456 = 100 * sum(N_TAXA[
(is.na(CLASS) == TRUE
| CLASS != "INSECTA")
& (is.na(ORDER) == TRUE
| ORDER != "TROMBIDIFORMES")
& (is.na(GENUS) == TRUE
| GENUS != "JUGA")
& (BCG_ATTR == "4"
| BCG_ATTR == "5"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pt_NonInsTrombJuga_BCG_att456 = 100 * nt_NonInsTrombJuga_BCG_att456 / nt_total
, nt_oneind = dplyr::n_distinct(TAXAID[N_TAXA == 1
& EXCLUDE != TRUE]
, na.rm = TRUE)
, pt_oneind = 100 * nt_oneind / nt_total
, nt_airbreath = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& AIRBREATHER == TRUE]
, na.rm = TRUE)
, pi_airbreath = 100 * sum(N_TAXA[AIRBREATHER == TRUE]
, na.rm = TRUE) / ni_total
, pt_airbreath = 100 * nt_airbreath / nt_total
# NM BCG
, ni_total_300 = 100 * (ni_total / 300)
, nt_Mol_Non_BCG_att6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PHYLUM == "MOLLUSCA"
& (is.na(BCG_ATTR)
| BCG_ATTR != "6")]
, na.rm = TRUE)
# WY, add to match MetricScores.xlsx
, pi_EphemNoBaeTri_RFadj = NA_real_
, nt_volt_semi_RFadj = NA_real_
, nt_COETNoBraBaeHydTri_RFadj = NA_real_
, x_BCICTQa_RFadjB = NA_real_
#
, .groups = "drop_last")## met.val.dni_F
##met.val, DNI = TRUE----
met.val.dni_T <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
#
# one metric per line
#
### totals----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0], na.rm = TRUE)
### DNI----
, nt_dni = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TAXAID == "DNI"]
, na.rm = TRUE)
, pi_dni = 100 * sum(N_TAXA[TAXAID == "DNI"]
, na.rm = TRUE) / ni_total
, pt_dni = 100 * nt_dni / nt_total
, .groups = "drop_last")## met.val.dni_T
## met.val, join----
cols2match <- c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS")
met_dni <- c("nt_dni", "pi_dni", "pt_dni")
met.val <- dplyr::left_join(met.val.dni_F
, met.val.dni_T[, c(cols2match, met_dni)])
}## IF ~ metric_subset
time_end2 <- Sys.time()
# difftime(time_end2, time_start2)
# dim(met.val)
#
# Clean Up ####
if (verbose == TRUE) {
debug_topic <- "clean up"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# replace NA with 0
#met.val[is.na(met.val)] <- 0
# but exclude SAMPLEID, INDEX_NAME INDEX_CLASS
# met.val <- met.val %>% dplyr::mutate(dplyr::across(where(is.numeric)
# , tidyr::replace_na
# , 0))
met.val <- as.data.frame(met.val)
met.val <- met.val %>% dplyr::mutate_if(is.numeric, tidyr::replace_na, 0)
# Crazy slow on tibble (several minutes) convert to data frame (< 2 seconds)
# met.val <- replace(is.na(met.val), 0)
# Marine Metrics
MetricNames_Marine <- c("nt_Capit"
, "nt_Caridea"
, "nt_Nereid"
, "nt_Nudib"
, "nt_Poly"
, "nt_PolyNoSpion"
, "nt_Spion"
, "pi_Amp"
, "pi_AmpHaust"
, "pi_Capit"
, "pi_Cirra"
, "pi_Clite"
, "pi_Haust"
, "pi_Hesion"
, "pi_Lucin"
, "pi_LucinTellin"
, "pi_Nereid"
, "pi_Nudib"
, "pi_Orbin"
, "pi_Poly"
, "pi_Spion"
, "pi_Spion2Poly"
, "pi_Tellin"
, "pi_Xanth"
, "pt_Nudib"
, "pt_Poly"
, "pt_PolyNoSpion"
, "pt_Spion"
, "rt_Amph"
, "rt_Bivalve"
, "rt_Capit"
, "rt_Car"
, "rt_Coleo"
, "rt_CruMol"
, "rt_Deca"
, "rt_Ephem"
, "rt_EPT"
, "rt_Gast"
, "rt_Isop"
, "rt_Nereid"
, "rt_Nudib"
, "rt_Oligo"
, "rt_Pleco"
, "rt_Poly"
, "rt_PolyNoSpion"
, "rt_Ptero"
, "rt_Spion"
, "rt_Trich"
, "rt_Tubif"
, "x_Becks_tv2"
)
## Subset ----
# # subset to only metrics specified by user
if (verbose == TRUE) {
debug_topic <- "subset"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(MetricNames)) {
# remove marine if MetrcNames not provided and boo.marine = false (default)
if (boo.marine == FALSE) {
met.val <- met.val[, !(names(met.val) %in% MetricNames_Marine)]
}## IF ~ boo.marine ~ END
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME",
"ni_total", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (verbose == TRUE) {
debug_topic <- "extra fields"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>%
dplyr::group_by(.dots = c("SAMPLEID", cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val)
, by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# df to report back
if (verbose == TRUE) {
debug_topic <- "return result"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
return(df.return)
}##FUNCTION.metric.values.bugs.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Fish
#'
#' @description Subfunction of metric.values for use with Fish.
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.fish <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, boo.Shiny
, verbose) {
# QC
boo_QC <- FALSE
if (boo_QC) {
myDF <- BioMonTools::data_fish_MBSS
MetricNames <- NULL
boo.Adjust <- FALSE
cols2keep <- NULL
boo.Shiny <- FALSE
verbose <- TRUE
}## IF ~ boo_QC
time_start <- Sys.time()
# not carrying over from previous?!
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "FISH"
boo_debug_sub <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 12
# global variable bindings ----
SAMPLEID <- INDEX_NAME <- INDEX_CLASS <- TAXAID <- N_TAXA <- NATIVE <-
HYBRID <- TYPE <- TROPHIC <- SILT <- TOLER <- N_ANOMALIES <- GENUS <-
FAMILY <- SAMP_WIDTH_M <- SAMP_LENGTH_M <- NULL
TROPHIC_GE <- TROPHIC_HB <- TROPHIC_IS <- TROPHIC_IV <- TROPHIC_OM <-
TROPHIC_TC <- NULL
ni_total <- x_Shan_e <- nt_total <- x_Evenness <- length_m <-
ni_natnonhybridnonmf <- ni_natnonhybridnonmfnonlepomis <- NULL
BCG_ATTR <- NULL
CONNECTIVITY <- SCC <- nt_AmmEthPerc <- nt_AmmEthPerc_Cott_Notur <-
nt_Cato <- nt_Cent <- nt_natCent <- nt_Cott <- nt_Cyprin <- nt_Ictal <-
nt_Lepomis <- nt_native <- nt_nonnative <- nt_Notur <- nt_Salm <-
nt_connect <- nt_scc <- TROPHIC_DE <- TROPHIC_PL <- nt_detritivore <-
nt_herbivore <- nt_omnivore <- nt_planktivore <- nt_topcarn <- area_m2 <-
ni_natnonhybridnonmfnonLepomis <- SAMP_BIOMASS <- ni_dom02 <- ni_dom03 <-
ni_dom04 <- ni_dom05 <- ni_dom06 <- ni_dom07 <- ni_dom08 <- ni_dom09 <-
ni_dom10 <- nt_BCG_att12 <- nt_BCG_att123 <- nt_BCG_att12346b <-
nt_BCG_att1236b <- nt_BCG_att2 <- nt_BCG_att2native <- nt_BCG_att23_scc <-
nt_BCG_att3 <- nt_BCG_att3native <- nt_BCG_att4 <- nt_BCG_att4native <-
nt_BCG_att5 <- nt_BCG_att5native <- nt_BCG_attNA <- TI_CORECOLD <-
TI_COLD <- TI_COOL <- TI_WARM <- TI_EURY <- TI_NA <- nt_ti_corecold <-
nt_ti_cold <- nt_ti_cool <- nt_ti_warm <- nt_ti_eury <- nt_ti_na <-
nt_ti_corecold_cold <- nt_ti_cool_warm <- ELEVATION_LOW <- ELEVATION_HIGH <-
GRADIENT_LOW <- GRADIENT_MOD <- GRADIENT_HIGH <- WSAREA_S <- WSAREA_M <-
WSAREA_L <- WSAREA_XL <- REPRO_BCAST <- REPRO_NS <- REPRO_NC <-
REPRO_BEAR <- REPRO_MIG <- HABITAT_B <- HABITAT_W <- nt_habitat_b <-
nt_habitat_w <- NULL
nt_natcoldwater <- nt_serialspawner <- nt_simplelithophil <- nt_tv_sens <-
nt_tv_senscoldwater <- nt_tv_toler <- nt_tv_vtoler <- nt_beninsct_notoler <-
pt_gen <- nt_gen <- nt_insectivore_notoler <- nt_darterscultpinsucker <-
nt_pioneer <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC ####
# Remove Non-Target Taxa
#myDF <- myDF[myDF[,"NonTarget"]==0,] # not relevant for fish
## QC, Missing Cols ----
if (verbose == TRUE) {
# 1
debug_topic <- "QC, required cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
, "FAMILY", "GENUS"
, "TYPE", "TOLER", "NATIVE", "TROPHIC", "SILT"
, "BCG_ATTR", "THERMAL_INDICATOR"
, "HABITAT", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR"
, "REPRODUCTION", "HABITAT", "CONNECTIVITY", "SCC"
, "BCG_ATTR2")
col.req_logical <- c("EXCLUDE", "HYBRID")
col.req_numeric <- c("N_TAXA", "N_ANOMALIES", "SAMP_BIOMASS", "DA_MI2"
, "SAMP_WIDTH_M", "SAMP_LENGTH_M", "TOLVAL2"
)
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
# col.req <- c("SAMPLEID", "TAXAID", "N_TAXA", "EXCLUDE"
# , "N_ANOMALIES", "SAMP_BIOMASS"
# , "INDEX_NAME", "INDEX_CLASS"
# , "DA_MI2", "SAMP_WIDTH_M", "SAMP_LENGTH_M"
# , "TYPE", "TOLER", "NATIVE", "TROPHIC", "SILT"
# , "FAMILY", "GENUS", "HYBRID", "BCG_ATTR", "THERMAL_INDICATOR"
# , "ELEVATION_ATTR", "GRADIENT_ATTR", "WSAREA_ATTR"
# , "REPRODUCTION", "HABITAT", "CONNECTIVITY", "SCC"
# )
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {##IF.num.col.req.missing.START
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the NATIVE field is missing all native related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" ", myPrompt.01, myPrompt.02, " ", myPrompt.03, myPrompt.04
, myPrompt.05, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive and boo.Shiny
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
myDF[, col.req.missing] <- NA
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Exclude"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "EXCLUDE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {
warn1 <- "EXCLUDE column does not have any TRUE values."
warn2 <- "This is common with fish samples."
warn3 <- "Valid values are TRUE or FALSE."
warn4 <- "Other values are not recognized"
msg <- paste(warn1, warn2, warn3, warn4, sep = "\n")
message(msg)
}##IF.Exclude.T.END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging ----
if (verbose == TRUE) {
# 2
debug_topic <- "Munge, values to upper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Column Values to UPPER case for met.val below
col2upper <- c("TAXAID" ,"FAMILY", "GENUS", "TYPE", "TOLER", "NATIVE"
, "TROPHIC", "THERMAL_INDICATOR", "ELEVATION_ATTR"
, "GRADIENT_ATTR", "WSAREA_ATTR", "REPRODUCTION", "HABITAT"
, "CONNECTIVITY", "SCC", "BCG_ATTR", "BCG_ATTR2")
for (i in col2upper) {
if (i %in% names(myDF)) {
myDF[, i] <- toupper(myDF[, i])
}## IF ~ i %in%
}##FOR ~ i col2upper
# Add extra columns for some fields
if (verbose == TRUE) {
# 4
debug_topic <- "Munge, TF"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "GE, IV" is both "GE" and "IV"
## HABITAT ----
if (!"HABITAT" %in% names(myDF)) {
myDF[, "HABITAT"] <- NA
}## IF ~ HABITAT
# Remove white space
myDF[, "HABITAT"] <- gsub(" ", "", myDF[, "HABITAT"])
# code new columns
myDF[, "HABITAT_B"] <- grepl("B", myDF[,"HABITAT"])
myDF[, "HABITAT_F"] <- grepl("F", myDF[,"HABITAT"]) # Fluvial
# W (MOD b/c of MN CW and CWN)
myDF[, "HABITAT_W"] <- grepl("^W$|^W,|,W$|,W,", myDF[,"HABITAT"])
# MN
myDF[, "HABITAT_CW"] <- grepl("^CW$|^CW,|CW$|,CW,", myDF[,"HABITAT"]) # CW
myDF[, "HABITAT_CWN"] <- grepl("CWN", myDF[,"HABITAT"]) # Coldwater, Native
myDF[, "HABITAT_HW_noT"] <- grepl("HW-T", myDF[,"HABITAT"]) # Headwater Specialist, no Tolerant
myDF[, "HABITAT_WE_noT"] <- grepl("WE-T", myDF[,"HABITAT"]) # Wetland, no Tolerant
## REPRODUCTION ----
if (!"REPRODUCTION" %in% names(myDF)) {
myDF[, "REPRODUCTION"] <- NA
}## IF ~ REPRODUCTION
# Remove white space
myDF[, "REPRODUCTION"] <- gsub(" ", "", myDF[, "REPRODUCTION"])
# code new columns
myDF[, "REPRO_BCAST"] <- grepl("BROADCASTER", myDF[,"REPRODUCTION"])
myDF[, "REPRO_NS"] <- grepl("SIMPLE NEST", myDF[,"REPRODUCTION"])
myDF[, "REPRO_NC"] <- grepl("COMPLEX NEST", myDF[,"REPRODUCTION"])
myDF[, "REPRO_BEAR"] <- grepl("BEARER", myDF[,"REPRODUCTION"])
myDF[, "REPRO_MIG"] <- grepl("MIGRATORY", myDF[,"REPRODUCTION"])
myDF[, "REPRO_LITH"] <- grepl("LITHOPHIL", myDF[,"REPRODUCTION"])
# MN
myDF[, "REPRO_MA2"] <- grepl("MA<2", myDF[,"REPRODUCTION"]) # Mature Age < 2
myDF[, "REPRO_MA3_noT"] <- grepl("MA>3-T", myDF[,"REPRODUCTION"]) # Mature Age > 3, no Tolerant
myDF[, "REPRO_NE"] <- grepl("NE", myDF[,"REPRODUCTION"]) # NonLithophilic Nester
myDF[, "REPRO_SER"] <- grepl("SER", myDF[,"REPRODUCTION"]) # Serial Spawner
myDF[, "REPRO_SILI"] <- grepl("SILI", myDF[,"REPRODUCTION"]) # Simple Lithophil
## THERMAL_INDICATOR----
if (!"THERMAL_INDICATOR" %in% names(myDF)) {
myDF[, "THERMAL_INDICATOR"] <- NA
}## IF ~ THERMAL_INDICATOR
# Remove white space
myDF[, "THERMAL_INDICATOR"] <- gsub(" ", "", myDF[, "THERMAL_INDICATOR"])
# code new columns
myDF[, "TI_CORECOLD"] <- grepl("COREC", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_COLD"] <- grepl("COLD", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_COOL"] <- grepl("COOL", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_WARM"] <- grepl("WARM", myDF[,"THERMAL_INDICATOR"])
myDF[, "TI_EURY"] <- grepl("EURYTHERMAL", myDF[,"THERMAL_INDICATOR"])
# exact matches only
myDF[, "TI_NA"] <- is.na(myDF[, "THERMAL_INDICATOR"])
## TOLER ----
if (!"TOLER" %in% names(myDF)) {
myDF[, "TOLER"] <- NA
}## IF ~ TOLER
# Remove white space
myDF[, "TOLER"] <- gsub(" ", "", myDF[, "TOLER"])
# code new columns
myDF[, "TOLER_TOLERANT"] <- grepl("TOLERANT", myDF[, "TOLER"]) # NOT USED
myDF[, "TOLER_INTOLERANT"] <- grepl("INTOLERANT", myDF[,"TOLER"]) # NOT USED
# MN
myDF[, "TOLER_ICW"] <- grepl("ICW", myDF[,"TOLER"])
myDF[, "TOLER_I"] <- grepl("^I$|^I,|,I$|,I,", myDF[,"TOLER"])
myDF[, "TOLER_ICW"] <- grepl("ICW", myDF[,"TOLER"])
myDF[, "TOLER_S"] <- grepl("^S$|^S,|,S$|,S,", myDF[,"TOLER"])
myDF[, "TOLER_SCW"] <- grepl("SCW", myDF[,"TOLER"])
myDF[, "TOLER_T"] <- grepl("^T$|^T,|,T$|,T,", myDF[,"TOLER"])
myDF[, "TOLER_TCW"] <- grepl("TCW", myDF[,"TOLER"])
myDF[, "TOLER_VT"] <- grepl("VT", myDF[,"TOLER"])
## TROPHIC ----
if (!"TROPHIC" %in% names(myDF)) {
myDF[, "TROPHIC"] <- NA
}## IF ~ TROPHIC
# Remove white space
myDF[, "TROPHIC"] <- gsub(" ", "", myDF[, "TROPHIC"])
# code new columns
myDF[, "TROPHIC_GE"] <- grepl("GE", myDF[, "TROPHIC"]) # Generalist
myDF[, "TROPHIC_HB"] <- grepl("HB|HE", myDF[, "TROPHIC"]) # Herbivore
myDF[, "TROPHIC_IS"] <- grepl("IS", myDF[, "TROPHIC"]) # Insectivore
myDF[, "TROPHIC_IV"] <- grepl("^IV$|^IV,|,IV$|,IV,", myDF[, "TROPHIC"]) # Invertivore
myDF[, "TROPHIC_OM"] <- grepl("OM", myDF[, "TROPHIC"]) # Omnivore
myDF[, "TROPHIC_TC"] <- grepl("^TC$|^TC,|,TC$|,TC,", myDF[, "TROPHIC"]) # Top Carnivore
myDF[, "TROPHIC_DE"] <- grepl("^DE$|^DE,|,DE$|,DE,", myDF[, "TROPHIC"]) # Detritivore (mod for DEM)
myDF[, "TROPHIC_PL"] <- grepl("PL", myDF[, "TROPHIC"]) # Planktivore
myDF[, "TROPHIC_PI"] <- grepl("PI", myDF[, "TROPHIC"]) # Piscivore
myDF[, "TROPHIC_IV_TC"] <- grepl("IV_TC", myDF[, "TROPHIC"]) # Invertivore and Top Carnivore
# MN
myDF[, "TROPHIC_BI_noT"] <- grepl("BI-T", myDF[, "TROPHIC"]) # Benthic Insectivore, no Tolerant
myDF[, "TROPHIC_IN_noT"] <- grepl("IN-T", myDF[, "TROPHIC"]) # Insectivore, no Tolerant
myDF[, "TROPHIC_IN_CYP"] <- grepl("INCYP", myDF[, "TROPHIC"]) # Insectivorous Cyprinidae
myDF[, "TROPHIC_DEM"] <- grepl("DEM", myDF[, "TROPHIC"]) # Detritivore Minor
## TYPE ----
if (!"TYPE" %in% names(myDF)) {
myDF[, "TYPE"] <- NA
}## IF ~ TYPE
# Remove white space
myDF[, "TYPE"] <- gsub(" ", "", myDF[, "TYPE"])
# code new columns
# Type is a catch all column so need to be specific in pattern match
# MN, Composition
myDF[, "TYPE_DSS"] <- grepl("^DSS$|^DSS,|,DSS$|,DSS,", myDF[,"TYPE"])
myDF[, "TYPE_DS"] <- grepl("^DS$|^DS,|,DS$|,DS,", myDF[,"TYPE"])
myDF[, "TYPE_EX"] <- grepl("^EX$|^EX,|,EX$|,EX,", myDF[,"TYPE"])
myDF[, "TYPE_MIN_noT"] <- grepl("^MIN-T$|^MIN-T,|,MIN-T$|,MIN-T,", myDF[,"TYPE"])
myDF[, "TYPE_PERC"] <- grepl("^PERC$|^PERC,|,PERC$|,PERC,", myDF[,"TYPE"])
# MN, Life History
myDF[, "TYPE_PI"] <- grepl("^PI$|^PI,|,PI$|,PI,", myDF[,"TYPE"])
myDF[, "TYPE_SL"] <- grepl("^SL$|^SL,|,SL$|,SL,", myDF[,"TYPE"])
# MN, Schooling
myDF[, "TYPE_SCHOOL"] <- grepl("^SCH$|^SCH,|,SCH$|,SCH,", myDF[,"TYPE"])
# MN, Brook Trout
myDF[, "TYPE_BROOKTROUT"] <- grepl("^BKT$|^BKT,|,BKT$|,BKT,", myDF[,"TYPE"])
# GP, Salt
myDF[, "TYPE_SALT"] <- grepl("SALT", myDF[, "TYPE"])
# GP, NPL
myDF[, "TYPE_NPL"] <- grepl("NPL", myDF[, "TYPE"])
## ELEVATION_ATTR ----
if (!"ELEVATION_ATTR" %in% names(myDF)) {
myDF[, "ELEVATION_ATTR"] <- NA
}## IF ~ ELEVATION_ATTR
# Remove white space
myDF[, "ELEVATION_ATTR"] <- gsub(" ", "", myDF[, "ELEVATION_ATTR"])
# code new columns
myDF[, "ELEVATION_LOW"] <- "LOW" == myDF[, "ELEVATION_ATTR"]
myDF[, "ELEVATION_HIGH"] <- "HIGH" == myDF[, "ELEVATION_ATTR"]
## GRADIENT_ATTR----
if (!"GRADIENT_ATTR" %in% names(myDF)) {
myDF[, "GRADIENT_ATTR"] <- NA
}## IF ~ GRADIENT_ATTR
# Remove white space
myDF[, "GRADIENT_ATTR"] <- gsub(" ", "", myDF[, "GRADIENT_ATTR"])
# code new columns
myDF[, "GRADIENT_LOW"] <- "LOW" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_MOD"] <- "MOD" == myDF[, "GRADIENT_ATTR"]
myDF[, "GRADIENT_HIGH"] <- "HIGH" == myDF[, "GRADIENT_ATTR"]
## WSAREA_ATTR ----
if (!"WSAREA_ATTR" %in% names(myDF)) {
myDF[, "WSAREA_ATTR"] <- NA
}## IF ~ WSAREA_ATTR
# Remove white space
myDF[, "WSAREA_ATTR"] <- gsub(" ", "", myDF[, "WSAREA_ATTR"])
# code new columns
myDF[, "WSAREA_S"] <- "SMALL" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_M"] <- "MEDIUM" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_L"] <- "LARGE" == myDF[, "WSAREA_ATTR"]
myDF[, "WSAREA_XL"] <- "XLARGE" == myDF[, "WSAREA_ATTR"]
## Create Dominant N ####
if (verbose == TRUE) {
# 4
debug_topic <- "Munge, Dom"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# DF for dom so same taxa get combined
myDF_dom <- dplyr::summarise(dplyr::group_by(myDF
, INDEX_NAME
, INDEX_CLASS
, SAMPLEID
, TAXAID
, TYPE_SCHOOL)
, N_TAXA = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# MN, add TYPE_SCHOOL, 20240601
# Create df for Top N (without ties)
#
df.dom01 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 1)
df.dom02 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 2)
df.dom03 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 3)
df.dom04 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 4)
df.dom05 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 5)
df.dom06 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 6)
df.dom07 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 7)
df.dom08 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 8)
df.dom09 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 9)
df.dom10 <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(dplyr::row_number() <= 10)
# MN
df_dom01_ExclSchool <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(TYPE_SCHOOL != TRUE) %>%
dplyr::filter(dplyr::row_number() <= 1)
df_dom02_ExclSchool <- dplyr::arrange(myDF_dom, SAMPLEID, dplyr::desc(N_TAXA)) %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::filter(TYPE_SCHOOL != TRUE) %>%
dplyr::filter(dplyr::row_number() <= 2)
# Summarise Top N
df.dom01.sum <- dplyr::summarise(dplyr::group_by(df.dom01
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom02.sum <- dplyr::summarise(dplyr::group_by(df.dom02
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom03.sum <- dplyr::summarise(dplyr::group_by(df.dom03
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom03 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom04.sum <- dplyr::summarise(dplyr::group_by(df.dom04
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom04 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom05.sum <- dplyr::summarise(dplyr::group_by(df.dom05
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom05 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom06.sum <- dplyr::summarise(dplyr::group_by(df.dom06
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom06 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom07.sum <- dplyr::summarise(dplyr::group_by(df.dom07
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom07 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom08.sum <- dplyr::summarise(dplyr::group_by(df.dom08
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom08 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom09.sum <- dplyr::summarise(dplyr::group_by(df.dom09
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom09 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df.dom10.sum <- dplyr::summarise(dplyr::group_by(df.dom10
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom10 = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# MN
df_dom01_ExclSchool_sum <- dplyr::summarise(dplyr::group_by(df_dom01_ExclSchool
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom01_ExclSchool = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
df_dom02_ExclSchool_sum <- dplyr::summarise(dplyr::group_by(df_dom02_ExclSchool
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
, ni_dom02_ExclSchool = sum(N_TAXA, na.rm = TRUE)
, .groups = "drop_last")
# Add column of domN to main DF
myDF <- merge(myDF, df.dom01.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom02.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom03.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom04.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom05.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom06.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom07.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom08.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom09.sum, all.x = TRUE)
myDF <- merge(myDF, df.dom10.sum, all.x = TRUE)
myDF <- merge(myDF, df_dom01_ExclSchool_sum, all.x = TRUE)
myDF <- merge(myDF, df_dom02_ExclSchool_sum, all.x = TRUE)
# Clean up extra Dom data frames
rm(myDF_dom)
rm(df.dom01)
rm(df.dom02)
rm(df.dom03)
rm(df.dom04)
rm(df.dom05)
rm(df.dom06)
rm(df.dom07)
rm(df.dom08)
rm(df.dom09)
rm(df.dom10)
rm(df_dom01_ExclSchool)
rm(df_dom02_ExclSchool)
rm(df.dom01.sum)
rm(df.dom02.sum)
rm(df.dom03.sum)
rm(df.dom04.sum)
rm(df.dom05.sum)
rm(df.dom06.sum)
rm(df.dom07.sum)
rm(df.dom08.sum)
rm(df.dom09.sum)
rm(df.dom10.sum)
rm(df_dom01_ExclSchool_sum)
rm(df_dom02_ExclSchool_sum)
## N_Anomalies ----
if (verbose == TRUE) {
# 5
debug_topic <- "Munge, anomalies"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# Munge N_Anomalies, NA to 0
myDF[, "N_ANOMALIES"] <- as.numeric(myDF[, "N_ANOMALIES"])
myDF[is.na(myDF[, "N_ANOMALIES"]), "N_ANOMALIES"] <- 0
# By taxon or sample total
# Data set up to have anomalies by taxon.
# But some report as sample total.
# This routine redistributes values proportionally to all taxa
# *IF* all are the same value
# Cases of same number of anomalies for all taxa should be rare but possible
stats_anom <- myDF %>%
dplyr::group_by(SAMPLEID) %>%
dplyr::summarize(n = dplyr::n()
, n_distinct = dplyr::n_distinct(N_ANOMALIES, na.rm = TRUE)
, mean = mean(N_ANOMALIES, na.rm = TRUE)
, sd = stats::sd(N_ANOMALIES, na.rm = TRUE)
, sum = sum(N_ANOMALIES, na.rm = TRUE))
stats_anom[, "SUM_ANOMALIES"] <- stats_anom[, "mean"] / stats_anom[, "n"]
# make change; n > 1 & n_distinct == 1
stats_anom$MOD_ANOMALIES <- ifelse(stats_anom$n > 1 &
stats_anom$n_distinct == 1, TRUE, FALSE)
# add back to myDF
myDF <- merge(myDF, stats_anom[, c("SAMPLEID"
, "SUM_ANOMALIES"
, "MOD_ANOMALIES")]
, all.x = TRUE)
myDF[myDF$MOD_ANOMALIES == TRUE, "N_ANOMALIES"] <- myDF[myDF$MOD_ANOMALIES == TRUE
, "SUM_ANOMALIES"]
# Metric Calc ####
if (verbose == TRUE) {
# 6
debug_topic <- "Calc, metrics"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# code above is different than benthos
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF, SAMPLEID, INDEX_NAME
, INDEX_CLASS, SAMP_WIDTH_M
, SAMP_LENGTH_M)
, .groups = "drop_last"
#
# MBSS 2005, 11 metrics
# (can do metrics as one step but MBSS output has
# numerator so will get that as well)
#
# when invoke a "x != abc" need to include "| is.na(x)"
# unless all "x" are populated (e.g., TRUE or FALSE)
## Individuals ####
# individuals, total
, ni_total = sum(N_TAXA, na.rm = TRUE)
, ni_total_notoler = sum(N_TAXA[TOLER != "TOLERANT" | is.na(TOLER)], na.rm = TRUE)
, ni_natnonhybridnonmf = sum(N_TAXA[NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID)) &
(TYPE != "MOSQUITOFISH" | is.na(TYPE))], na.rm = TRUE)
, ni_natnonhybridnonmfnonLepomis = sum(N_TAXA[NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID)) &
(TYPE != "MOSQUITOFISH" | is.na(TYPE)) &
(GENUS != "LEPOMIS" | is.na(GENUS))], na.rm = TRUE)
#
## Percent Individuals ####
, pi_AmmEthPerc = 100 * sum(N_TAXA[GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"], na.rm = TRUE) / ni_total
, pi_AmmEthPerc_Cott_Notur = 100 * sum(N_TAXA[(GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"
| GENUS == "NOTURUS")
| FAMILY == "COTTIDAE"]
, na.rm = TRUE) / ni_total
# % Round-Bodied Suckers
, pi_rbs = 100 * sum(N_TAXA[TYPE == "RBS"], na.rm = TRUE) / ni_total
, pi_brooktrout = 100 * sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) / ni_total
, pi_brooktrout_wild = 100 * sum(N_TAXA[TAXAID == "BROOK TROUT, WILD"], na.rm = TRUE) / ni_total
, pi_Cato = 100 * sum(N_TAXA[FAMILY == "CATOSTOMIDAE"], na.rm = TRUE) / ni_total
, pi_Cent = 100 * sum(N_TAXA[FAMILY == "CENTRARCHIDAE"], na.rm = TRUE) / ni_total
, pi_natCent = 100 * sum(N_TAXA[NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE) / ni_total
, pi_Cott = 100 * sum(N_TAXA[FAMILY == "COTTIDAE"], na.rm = TRUE) / ni_total
, pi_Cyprin = 100 * sum(N_TAXA[FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
, pi_Ictal = 100 * sum(N_TAXA[FAMILY == "ICTALURIDAE"], na.rm = TRUE) / ni_total
, pi_native = 100 * sum(N_TAXA[NATIVE == "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative = 100 * sum(N_TAXA[is.na(NATIVE) | NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative_NotNativeNotNA = 100 * sum(N_TAXA[NATIVE != "NATIVE"], na.rm = TRUE) / ni_total
, pi_nonnative_OnlyNonNative = 100 * sum(N_TAXA[NATIVE == "NON-NATIVE"], na.rm = TRUE) / ni_total
, pi_Notur = 100 * sum(N_TAXA[GENUS == "NOTURUS"], na.rm = TRUE) / ni_total
, pi_sculpin = 100 * sum(N_TAXA[TYPE == "SCULPIN"], na.rm = TRUE) / ni_total
, pi_Lepomis = 100 * sum(N_TAXA[GENUS == "LEPOMIS"], na.rm = TRUE) / ni_total
, pi_Salm = 100 * sum(N_TAXA[FAMILY == "SALMONIDAE"], na.rm = TRUE) / ni_total
, pi_trout = 100 * sum(N_TAXA["TROUT" %in% TYPE], na.rm = TRUE) / ni_total
, pi_brooktrout_BCG_att6 = 100 * (sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "6"], na.rm = TRUE)) / ni_total
, pi_connect = 100 * sum(N_TAXA[CONNECTIVITY == TRUE], na.rm = TRUE) / ni_total
, pi_scc = 100 * sum(N_TAXA[SCC == TRUE], na.rm = TRUE) / ni_total
, pi_brooktrout2brooktrout_BCG_att6 = 100 *
sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) /
(sum(N_TAXA[TYPE_BROOKTROUT == TRUE], na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "6"], na.rm = TRUE))
# benthic fluvial specialist
, pi_bfs = 100 * sum(N_TAXA[(TYPE == "BENTHIC" & TROPHIC_IV == TRUE) |
TYPE == "RBS" | TYPE == "SMM"], na.rm = TRUE) / ni_total
#
## Number of Taxa ####
# account for "NONE" in nt_total, should be the only 0 N_TAXA
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & N_TAXA > 0], na.rm = TRUE)
#, nt_benthic=dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TYPE == "DARTER" | TYPE == "SCULPIN" | TYPE == "MADTOM" | TYPE == "LAMPREY"])
, nt_benthic = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TYPE == "BENTHIC"], na.rm = TRUE)
, nt_AmmEthPerc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA")], na.rm = TRUE)
, nt_AmmEthPerc_Cott_Notur = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (GENUS == "AMMOCRYPTA"
| GENUS == "ETHEOSTOMA"
| GENUS == "PERCINA"
| GENUS == "NOTURUS")
| FAMILY == "COTTIDAE"]
, na.rm = TRUE)
, nt_Cato = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CATOSTOMIDAE"], na.rm = TRUE)
, nt_Cent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_natCent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_Cott = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "COTTIDAE"], na.rm = TRUE)
, nt_Cyprin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_natCyprin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_Lepomis = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GENUS == "LEPOMIS"], na.rm = TRUE)
, nt_native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & N_TAXA > 0], na.rm = TRUE)
, nt_nonnative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (is.na(NATIVE) | NATIVE != "NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nonnative_NotNativeNotNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (NATIVE != "NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nonnative_OnlyNonNative = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (NATIVE == "NON-NATIVE")
& N_TAXA > 0], na.rm = TRUE)
, nt_nativenonhybrid = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
(HYBRID != TRUE | is.na(HYBRID))], na.rm = TRUE)
, nt_Notur = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GENUS == "NOTURUS"], na.rm = TRUE)
, nt_Ictal = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "ICTALURIDAE"], na.rm = TRUE)
, nt_natsunfish = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & TYPE == "SUNFISH"], na.rm = TRUE)
, nt_natCent_sunfish = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
(TYPE == "SUNFISH" | TYPE == "CENTRARCHIDAE")], na.rm = TRUE)
, nt_natCent = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & FAMILY == "CENTRARCHIDAE"], na.rm = TRUE)
, nt_natinsctCypr = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" &
TROPHIC_IS == TRUE & FAMILY == "CYPRINIDAE"], na.rm = TRUE)
, nt_natrbs = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & NATIVE == "NATIVE" & TYPE == "RBS"], na.rm = TRUE)
, nt_Petro = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "PETROMYZONTIDAE"], na.rm = TRUE)
, nt_Salm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & FAMILY == "SALMONIDAE"], na.rm = TRUE)
, nt_connect = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & CONNECTIVITY == TRUE], na.rm = TRUE)
, nt_scc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & SCC == TRUE], na.rm = TRUE)
, nt_beninsct_nows_nobg = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TROPHIC_IS == TRUE
& (TAXAID != "CATOSTOMUS COMMERSONII"
| TAXAID != "LEPOMIS MACROCHIRUS"
| is.na(TAXAID))
], na.rm = TRUE)
, nt_trout_sunfish_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ("TROUT" %in% TYPE
| TYPE == "SUNFISH")
& (TOLER != "TOLERANT"
| is.na(TOLER))
], na.rm = TRUE)
# , nt_beninsct_nows_nobg = NA
# , nt_trout_sunfish_notoler = NA
# , pi_pisc_noae = NA
## Percent of Taxa ----
, pt_AmmEthPerc = 100 * nt_AmmEthPerc / nt_total
, pt_AmmEthPerc_Cott_Notur = 100 * nt_AmmEthPerc_Cott_Notur / nt_total
, pt_Cato = 100 * nt_Cato / nt_total
, pt_Cent = 100 * nt_Cent / nt_total
, pt_natCent = 100 * nt_natCent / nt_total
, pt_Cott = 100 * nt_Cott / nt_total
, pt_Cyprin = 100 * nt_Cyprin / nt_total
, pt_Ictal = 100 * nt_Ictal / nt_total
, pt_Lepomis = 100 * nt_Lepomis / nt_total
, pt_native = 100 * nt_native / nt_total
, pt_nonnative = 100 * nt_nonnative / nt_total
, pt_nonnative_NotNativeNotNA = 100 * nt_nonnative_NotNativeNotNA / nt_total
, pt_nonnative_OnlyNonNative = 100 * nt_nonnative_OnlyNonNative / nt_total
, pt_Notur = 100 * nt_Notur / nt_total
, pt_Salm = 100 * nt_Salm / nt_total
, pt_connect = 100 * nt_connect / nt_total
, pt_scc = 100 * nt_scc / nt_total
## Trophic ####
### Trophic, nt----
, nt_beninvert = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE == "BENTHIC"
& TROPHIC_IV == TRUE]
, na.rm = TRUE)
, nt_habitat_beninvert = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV == TRUE
& HABITAT_B == TRUE]
, na.rm = TRUE)
, nt_detritivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_DE == TRUE]
, na.rm = TRUE)
, nt_herbivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_HB == TRUE]
, na.rm = TRUE)
, nt_invertivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV == TRUE]
, na.rm = TRUE)
, nt_inverttopcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IV_TC == TRUE]
, na.rm = TRUE)
, nt_omnivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_OM == TRUE]
, na.rm = TRUE)
, nt_planktivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PL == TRUE
], na.rm = TRUE)
, nt_topcarn = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_TC == TRUE]
, na.rm = TRUE)
, nt_piscivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PI == TRUE]
, na.rm = TRUE)
### Trophic, pi----
# % Lithophilic spawners
, pi_lithophil = 100 * sum(N_TAXA[SILT == TRUE], na.rm = TRUE) / ni_total
, pi_habitat_beninvert = 100 * sum(N_TAXA[TROPHIC_IV == TRUE
& HABITAT_B == TRUE], na.rm = TRUE) / ni_total
, pi_detritivore = 100 * sum(N_TAXA[TROPHIC_DE == TRUE], na.rm = TRUE) / ni_total
# % gen, omn, invert
, pi_gen = 100 * sum(N_TAXA[TROPHIC_GE == TRUE], na.rm = TRUE) / ni_total
, pi_genherb = 100 * sum(N_TAXA[TROPHIC_GE == TRUE | TROPHIC_HB == TRUE], na.rm = TRUE) / ni_total
, pi_genomninvrt = 100 * sum(N_TAXA[TROPHIC_GE == TRUE | TROPHIC_OM == TRUE | TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
, pi_herbivore = 100 * sum(N_TAXA[TROPHIC_HB == TRUE], na.rm = TRUE) / ni_total
, pi_insectivore = 100 * sum(N_TAXA[TROPHIC_IS == TRUE], na.rm = TRUE) / ni_total
, pi_insctCypr = 100 * sum(N_TAXA[TROPHIC_IS == TRUE &
FAMILY == "CYPRINIDAE"], na.rm = TRUE) / ni_total
, pi_invertivore = 100 * sum(N_TAXA[TROPHIC_IV == TRUE], na.rm = TRUE) / ni_total
, pi_inverttopcarn = 100 * sum(N_TAXA[TROPHIC_IV_TC == TRUE], na.rm = TRUE) / ni_total
, pi_omnivore = 100 * sum(N_TAXA[TROPHIC_OM == TRUE], na.rm = TRUE) / ni_total
, pi_planktivore = 100 * sum(N_TAXA[TROPHIC_PL == TRUE], na.rm = TRUE) / ni_total
, pi_topcarn = 100 * sum(N_TAXA[TROPHIC_TC == TRUE], na.rm = TRUE) / ni_total
, pi_trout = 100 * sum(N_TAXA["TROUT" %in% TYPE], na.rm = TRUE) / ni_total
, pi_pisc_noae = 100 * sum(N_TAXA[TYPE == "PISCIVORE"
& (TAXAID != "ANGUILLA ROSTRATA"
| is.na(TAXAID))], na.rm = TRUE) / ni_total
### Trophic, pt ----
, pt_habitat_beninvert = 100 * nt_habitat_beninvert / nt_total
, pt_detritivore = 100 * nt_detritivore / nt_total
, pt_herbivore = 100 * nt_herbivore / nt_total
, pt_invertivore = 100 * nt_invertivore / nt_total
, pt_inverttopcarn = 100 * nt_inverttopcarn / nt_total
, pt_omnivore = 100 * nt_omnivore / nt_total
, pt_planktivore = 100 * nt_planktivore / nt_total
, pt_topcarn = 100 * nt_topcarn / nt_total
#
## Tolerance ####
, nt_tv_intol = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & TOLER == "INTOLERANT"], na.rm = TRUE)
, nt_tv_intolhwi = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & (TOLER == "INTOLERANT" |
TOLER == "HWI")], na.rm = TRUE)
, pi_tv_toler = 100 * sum(N_TAXA[TOLER == "TOLERANT"], na.rm = TRUE) / ni_total
#
## Indices ####
# Shannon-Weiner
#, x_Shan_Num= -sum(log(N_TAXA / ni_total)), na.rm = TRUE)
#, x_Shan_e=x_Shan_Num/log(exp(1))
, x_Shan_e = -sum((N_TAXA / ni_total)*log((N_TAXA / ni_total)), na.rm = TRUE)
, x_Shan_2 = x_Shan_e/log(2)
, x_Shan_10 = x_Shan_e/log(10)
, x_Evenness = x_Shan_e/log(nt_total)
, x_Evenness100_ni99gt = ifelse(ni_total < 100, 1, x_Evenness * 100)
#
## Other ----
, length_m = max(SAMP_LENGTH_M, na.rm = TRUE)
, area_m2 = max(SAMP_WIDTH_M, na.rm = TRUE) * length_m
### Abund / sq meter
, ni_m2 = ni_total / area_m2 #/(StWidAvg*StLength)
, ni_200m = 200 * ni_total / length_m
, ni_natnonhybridnonmf_200m = 200 * ni_natnonhybridnonmf / length_m
, ni_natnonhybridnonmfnonLepomis_200m = 200 * ni_natnonhybridnonmfnonLepomis / length_m
# biomass per square meter (assumes sample not individual biomass)
, biomass_m2 = max(SAMP_BIOMASS, na.rm = TRUE) / area_m2 #/(StWidAvg*StLength)
### Anomalies
, pi_anomalies = 100 * sum(N_ANOMALIES, na.rm = TRUE) / ni_total
, pi_delt = 100 * sum(N_ANOMALIES, na.rm = TRUE) / ni_total
## Dominant N ####
## uses previously defined values added to myDF
, pi_dom01 = 100 * max(N_TAXA, na.rm = TRUE) / ni_total
, pi_dom02 = 100 * max(ni_dom02, na.rm = TRUE) / ni_total
, pi_dom03 = 100 * max(ni_dom03, na.rm = TRUE) / ni_total
, pi_dom04 = 100 * max(ni_dom04, na.rm = TRUE) / ni_total
, pi_dom05 = 100 * max(ni_dom05, na.rm = TRUE) / ni_total
, pi_dom06 = 100 * max(ni_dom06, na.rm = TRUE) / ni_total
, pi_dom07 = 100 * max(ni_dom07, na.rm = TRUE) / ni_total
, pi_dom08 = 100 * max(ni_dom08, na.rm = TRUE) / ni_total
, pi_dom09 = 100 * max(ni_dom09, na.rm = TRUE) / ni_total
, pi_dom10 = 100 * max(ni_dom10, na.rm = TRUE) / ni_total
## BCG ####
### BCG, nt ----
, nt_BCG_att1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "1"]
, na.rm = TRUE)
, nt_BCG_att12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE)
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG2_att123b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR2 == "3_BETTER")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG2_att1234b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att1236 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att1236b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6B")]
, na.rm = TRUE)
, nt_BCG_att12346 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att12346b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6B")]
, na.rm = TRUE)
, nt_BCG_att1i236i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE)
, nt_BCG_att2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "2"]
, na.rm = TRUE)
, nt_BCG_att2native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "2"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att23_scc = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "2"
| BCG_ATTR == "3")
& SCC == TRUE]
, na.rm = TRUE)
, nt_BCG_att3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "3"]
, na.rm = TRUE)
, nt_BCG_att3native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "3"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "4"]
, na.rm = TRUE)
, nt_BCG_att4native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "4"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att4b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE)
, nt_BCG_att4m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE)
, nt_BCG_att4w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE)
, nt_BCG_att4w5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "5"]
, na.rm = TRUE)
, nt_BCG_att5native = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "5"
& NATIVE == "NATIVE"]
, na.rm = TRUE)
, nt_BCG_att55a6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6")]
, na.rm = TRUE)
, nt_BCG_att55a6a = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE)
, nt_BCG_att56t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_BCG_att6i = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6I"]
, na.rm = TRUE)
, nt_BCG_att6m = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6M"]
, na.rm = TRUE)
, nt_BCG_att6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BCG_ATTR == "6T"]
, na.rm = TRUE)
, nt_BCG_attNA = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& is.na(BCG_ATTR)]
, na.rm = TRUE)
### BCG, pi ----
, pi_BCG_att12 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2")]
, na.rm = TRUE) / ni_total
, pi_BCG_att123 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1234 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_BCG2_att1234b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1236 = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1236sp = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6")]
, na.rm = TRUE) / sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6"
| BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE)
, pi_BCG_att1236b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att12346b = 100 * sum(N_TAXA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att1i236i = 100 * sum(N_TAXA[(BCG_ATTR == "1I"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "6I")]
, na.rm = TRUE) / ni_total
, pi_BCG_att2 = 100 * sum(N_TAXA[BCG_ATTR == "2"]
, na.rm = TRUE) / ni_total
, pi_BCG_att2native = 100 * sum(N_TAXA[BCG_ATTR == "2"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att23_scc = 100 * sum(N_TAXA[(BCG_ATTR == "2"
| BCG_ATTR == "3")
& SCC == TRUE]
, na.rm = TRUE) / ni_total
, pi_BCG_att3 = 100 * sum(N_TAXA[BCG_ATTR == "3"]
, na.rm = TRUE) / ni_total
, pi_BCG_att3native = 100 * sum(N_TAXA[BCG_ATTR == "3"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4 = 100 * sum(N_TAXA[BCG_ATTR == "4"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4native = 100 * sum(N_TAXA[BCG_ATTR == "4"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att4b = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_BETTER")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4m = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_MIDDLE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w = 100 * sum(N_TAXA[(BCG_ATTR2 == "4_WORSE")]
, na.rm = TRUE) / ni_total
, pi_BCG_att4w5 = 100 * (sum(N_TAXA[BCG_ATTR2 == "4_WORSE"]
, na.rm = TRUE) +
sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE)) / ni_total
, pi_BCG_att5 = 100 * sum(N_TAXA[BCG_ATTR == "5"]
, na.rm = TRUE) / ni_total
, pi_BCG_att5native = 100 * sum(N_TAXA[BCG_ATTR == "5"
& NATIVE == "NATIVE"]
, na.rm = TRUE) / ni_total
, pi_BCG_att55a6a = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56a = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att5a6a = 100 * sum(N_TAXA[(BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att56t = 100 * sum(N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6T")]
, na.rm = TRUE) / ni_total
, pi_BCG_att6 = 100 * sum(N_TAXA[BCG_ATTR == "6"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6i = 100 * sum(N_TAXA[BCG_ATTR == "6I"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6m = 100 * sum(N_TAXA[BCG_ATTR == "6M"]
, na.rm = TRUE) / ni_total
, pi_BCG_att6t = 100 * sum(N_TAXA[BCG_ATTR == "6T"]
, na.rm = TRUE) / ni_total
, pi_BCG_att66a = 100 * sum(N_TAXA[(BCG_ATTR == "6"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_BCG_att66a6b = 100 * sum(N_TAXA[(BCG_ATTR == "6"
| BCG_ATTR == "6A"
| BCG_ATTR == "6B")]
, na.rm = TRUE) / ni_total
, pi_BCG_att66s6t = 100 * sum(N_TAXA[BCG_ATTR == "6"
| BCG_ATTR == "6S"
| BCG_ATTR == "6T"]
, na.rm = TRUE) / ni_total
, pi_BCG_attNA = 100 * sum(N_TAXA[is.na(BCG_ATTR)]
, na.rm = TRUE) / ni_total
### BCG, pt----
, pt_BCG_att12 = 100 * nt_BCG_att12 / nt_total
, pt_BCG_att123 = 100 * nt_BCG_att123 / nt_total
, pt_BCG2_att123b = 100 * nt_BCG2_att123b / nt_total
, pt_BCG_att1234 = 100 * nt_BCG_att1234 / nt_total
, pt_BCG2_att1234b = 100 * nt_BCG2_att1234b / nt_total
, pt_BCG_att1236 = 100 * nt_BCG_att1236 / nt_total
, pt_BCG_att1236b = 100 * nt_BCG_att1236b / nt_total
, pt_BCG_att1236sp = 100 * nt_BCG_att1236 / (nt_BCG_att1236 +
nt_BCG_att55a6a)
, pt_BCG_att12346b = 100 * nt_BCG_att12346b / nt_total
, pt_BCG_att1i236i = 100 * nt_BCG_att1i236i / nt_total
, pt_BCG_att2 = 100 * nt_BCG_att2 / nt_total
, pt_BCG_att2native = 100 * nt_BCG_att2native / nt_total
, pt_BCG_att23_scc = 100 * nt_BCG_att23_scc / nt_total
, pt_BCG_att3 = 100 * nt_BCG_att3 / nt_total
, pt_BCG_att3native = 100 * nt_BCG_att3native / nt_total
, pt_BCG_att4 = 100 * nt_BCG_att4 / nt_total
, pt_BCG_att4native = 100 * nt_BCG_att4native / nt_total
, pt_BCG_att4b = 100 * nt_BCG_att4b / nt_total
, pt_BCG_att4m = 100 * nt_BCG_att4m / nt_total
, pt_BCG_att4w = 100 * nt_BCG_att4w / nt_total
, pt_BCG_att4w5 = 100 * nt_BCG_att4w5 / nt_total
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
, pt_BCG_att5native = 100 * nt_BCG_att5native / nt_total
, pt_BCG_att55a6a = 100 * nt_BCG_att55a6 / nt_total
, pt_BCG_att56t = 100 * nt_BCG_att56t / nt_total
, pt_BCG_att6i = 100 * nt_BCG_att6i / nt_total
, pt_BCG_att6m = 100 * nt_BCG_att6m / nt_total
, pt_BCG_att6t = 100 * nt_BCG_att6t / nt_total
, pt_BCG_attNA = 100 * nt_BCG_attNA / nt_total
### BCG, pi_dom----
, pi_dom01_BCG_att4 = 100 * max(0
, N_TAXA[(BCG_ATTR == "4")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att45 = 100 * max(0
, N_TAXA[(BCG_ATTR == "4"
| BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5 = 100 * max(0
, N_TAXA[(BCG_ATTR == "5")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5a = 100 * max(0
, N_TAXA[(BCG_ATTR == "5A")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att5a6a = 100 * max(0
, N_TAXA[(BCG_ATTR == "5A"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
, pi_dom01_BCG_att566a = 100 * max(0, N_TAXA[(BCG_ATTR == "5"
| BCG_ATTR == "6"
| BCG_ATTR == "6A")]
, na.rm = TRUE) / ni_total
## Thermal Indicators ####
## nt_ti
, nt_ti_corecold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_CORECOLD == TRUE]
, na.rm = TRUE)
, nt_ti_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COLD == TRUE]
, na.rm = TRUE)
, nt_ti_cool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_COOL == TRUE]
, na.rm = TRUE)
, nt_ti_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_WARM == TRUE]
, na.rm = TRUE)
, nt_ti_eury = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_EURY == TRUE]
, na.rm = TRUE)
, nt_ti_na = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TI_NA == TRUE]
, na.rm = TRUE)
, nt_ti_corecold_cold = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_CORECOLD == TRUE
| TI_COLD == TRUE)]
, na.rm = TRUE)
, nt_ti_cool_warm = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TI_COOL == TRUE
| TI_WARM == TRUE)]
, na.rm = TRUE)
## pi_ti
, pi_ti_corecold = 100 * sum(N_TAXA[TI_CORECOLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cold = 100 * sum(N_TAXA[TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool = 100 * sum(N_TAXA[TI_COOL == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_warm = 100 * sum(N_TAXA[TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_eury = 100 * sum(N_TAXA[TI_EURY == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_na = 100 * sum(N_TAXA[TI_NA == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_corecold_cold = 100 * sum(N_TAXA[TI_CORECOLD == TRUE |
TI_COLD == TRUE]
, na.rm = TRUE) / ni_total
, pi_ti_cool_warm = 100 * sum(N_TAXA[TI_COOL == TRUE |
TI_WARM == TRUE]
, na.rm = TRUE) / ni_total
## pt_ti
, pt_ti_corecold = 100 * nt_ti_corecold / nt_total
, pt_ti_cold = 100 * nt_ti_cold / nt_total
, pt_ti_cool = 100 * nt_ti_cool / nt_total
, pt_ti_warm = 100 * nt_ti_warm / nt_total
, pt_ti_eury = 100 * nt_ti_eury / nt_total
, pt_ti_na = 100 * nt_ti_na / nt_total
, pt_ti_corecold_cold = 100 * nt_ti_corecold_cold / nt_total
, pt_ti_cool_warm = 100 * nt_ti_cool_warm / nt_total
## Elevation ----
, nt_elev_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ELEVATION_LOW == TRUE]
, na.rm = TRUE)
, nt_elev_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & ELEVATION_HIGH == TRUE]
, na.rm = TRUE)
## Gradient ----
, nt_grad_low = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_LOW == TRUE]
, na.rm = TRUE)
, nt_grad_mod = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_MOD == TRUE]
, na.rm = TRUE)
, nt_grad_high = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & GRADIENT_HIGH == TRUE]
, na.rm = TRUE)
## WS_Area ----
, nt_wsarea_small = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_S == TRUE]
, na.rm = TRUE)
, nt_wsarea_medium = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_M == TRUE]
, na.rm = TRUE)
, nt_wsarea_large = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_L == TRUE]
, na.rm = TRUE)
, nt_wsarea_xlarge = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & WSAREA_XL == TRUE]
, na.rm = TRUE)
## Reproduction ----
### Repro, nt ----
, nt_repro_broadcaster = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_BCAST == TRUE]
, na.rm = TRUE)
, nt_repro_nestsimp = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_NS == TRUE]
, na.rm = TRUE)
, nt_repro_nestcomp = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_NC == TRUE]
, na.rm = TRUE)
, nt_repro_bearer = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_BEAR == TRUE]
, na.rm = TRUE)
, nt_repro_migratory = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_MIG == TRUE]
, na.rm = TRUE)
, nt_repro_lithophil = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & REPRO_LITH == TRUE]
, na.rm = TRUE)
### Repro, pi ----
, pi_repro_broadcaster = 100 * sum(N_TAXA[REPRO_BCAST == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_nestsimp = 100 * sum(N_TAXA[REPRO_NS == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_nestcomp = 100 * sum(N_TAXA[REPRO_NC == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_bearer = 100 * sum(N_TAXA[REPRO_BEAR == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_migratory = 100 * sum(N_TAXA[REPRO_MIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_repro_lithophil = 100 * sum(N_TAXA[REPRO_LITH == TRUE]
, na.rm = TRUE) / ni_total
### Repro, pt ----
, pt_repro_broadcaster = 100 * nt_repro_broadcaster / nt_total
, pt_repro_nestsimp = 100 * nt_repro_nestsimp / nt_total
, pt_repro_nestcomp = 100 * nt_repro_nestcomp / nt_total
, pt_repro_bearer = 100 * nt_repro_bearer / nt_total
, pt_repro_migratory = 100 * nt_repro_migratory / nt_total
, pt_repro_lithophil = 100 * nt_repro_lithophil / nt_total
## Habitat ####
# BCG Great Plains 2021
# W = water column
# B = benthic
# F = fluvial
#
# nt_habitat
, nt_habitat_b = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_B == TRUE]
, na.rm = TRUE)
, nt_habitat_w = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_W == TRUE]
, na.rm = TRUE)
, nt_habitat_f = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE & HABITAT_F == TRUE]
, na.rm = TRUE)
## pi_habitat
, pi_habitat_b = 100 * sum(N_TAXA[HABITAT_B == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_w = 100 * sum(N_TAXA[HABITAT_W == TRUE]
, na.rm = TRUE) / ni_total
, pi_habitat_f = 100 * sum(N_TAXA[HABITAT_F == TRUE]
, na.rm = TRUE) / ni_total
## pt_habitat
, pt_habitat_b = 100 * nt_habitat_b / nt_total
, pt_habitat_w = 100 * nt_habitat_w / nt_total
, pt_habitat_f = 100 * nt_habitat_f / nt_total
## SPECIAL ----
# odd ball metrics that don't fit the above groupings
# OR are really different and probably only applicable
# to a specific entity
#### New Mexico Fish BCG
, nt_piscivore_BCG_att66s6t = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_PI == TRUE
& (BCG_ATTR == "6"
| BCG_ATTR == "6S"
| BCG_ATTR == "6T")]
, na.rm = TRUE)
, nt_LLNLB = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE == "LLNLB"]
, na.rm = TRUE)
, nt_Cyprin_BCG_att1234 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& FAMILY == "CYPRINIDAE"
& (BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, ni_Hybognathus_amarus = sum(N_TAXA[TAXAID == "HYBOGNATHUS AMARUS"]
, na.rm = TRUE)
, x_TrophicCats = dplyr::n_distinct(TROPHIC, na.rm = TRUE)
### Great Plains BCG, 2024-04-25
, x_BCG_Mean = mean(TOLVAL2, na.rm = TRUE)
, nt_PupKilli = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TAXAID == "CYPRINODON RUBROFLUVIATILIS" #RED RIVER PUPFISH
| TAXAID == "FUNDULUS KANSAE" #NORTHERN PLAINS KILLIFISH
| TAXAID == "FUNDULUS ZEBRINUS")] #PLAINS KILLIFISH
, na.rm = TRUE)
# Great Plains 2024-08-06
#### GP, SALT
, pi_salt = 100 * sum(N_TAXA[TYPE_SALT == TRUE]
, na.rm = TRUE) / ni_total
#### GP, NPL
, pi_NPL = 100 * sum(N_TAXA[TYPE_NPL == TRUE]
, na.rm = TRUE) / ni_total
### Minnesota (Red Lakes) FIBI, 2024-06-01----
#### MN, nt
, nt_total_ExclSchool = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0
& TYPE_SCHOOL != TRUE]
, na.rm = TRUE)
#### MN, ni
, ni_total_ExclSchool = sum(N_TAXA[TYPE_SCHOOL != TRUE]
, na.rm = TRUE)
, ni_total_notoler_mn = sum(N_TAXA[TOLER_T != TRUE]
, na.rm = TRUE)
#### MN, nt, HABITAT
, nt_coldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_CW == TRUE]
, na.rm = TRUE)
, nt_natcoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_CWN == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_hw_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_HW_noT == TRUE]
, na.rm = TRUE)
, nt_wetland_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HABITAT_WE_noT == TRUE]
, na.rm = TRUE)
#### MN, nt, REPRO
, nt_serialspawner = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& REPRO_SER == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_simplelithophil = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& REPRO_SILI == TRUE]
, na.rm = TRUE)
#### MN, nt, TOLER
, nt_tv_sens = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_S == TRUE]
, na.rm = TRUE)
, nt_tv_senscoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_SCW == TRUE]
, na.rm = TRUE)
, nt_tv_tolercoldwater = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_TCW == TRUE]
, na.rm = TRUE)
, nt_tv_toler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_T == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_tv_vtoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLER_VT == TRUE]
, na.rm = TRUE)
#### MN, nt, TROPHIC
, nt_beninsct_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_BI_noT == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_detritivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_DE == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_gen = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_GE == TRUE]
, na.rm = TRUE)
, nt_insectivore_notoler = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_IN_noT == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_omnivore = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_OM == TRUE]
, na.rm = TRUE) # MN, nt for pt
#### MN, nt, TYPE
, nt_dartersculpin = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_DS == TRUE]
, na.rm = TRUE)
, nt_darterscultpinsucker = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_DSS == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_pioneer = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_PI == TRUE]
, na.rm = TRUE) # MN, nt for pt
, nt_shortlived = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TYPE_SL == TRUE]
, na.rm = TRUE)
### MN, pi, HABITAT
, pi_hw_notoler_ExclSchool = 100 * sum(N_TAXA[HABITAT_HW_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_wetland_notoler_ExclSchool = 100 * sum(N_TAXA[HABITAT_WE_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_natcoldwater_ExclSchool = 100 * sum(N_TAXA[HABITAT_CWN == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, REPRO
, pi_ma2_ExclShool = 100 * sum(N_TAXA[REPRO_MA2 == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_ma3_notoler_ExclSchool = 100 * sum(N_TAXA[REPRO_MA3_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_nonlithophil_ExclSchool = 100 * sum(N_TAXA[REPRO_NE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_serialspawner_ExclSchool = 100 * sum(N_TAXA[REPRO_SER == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_simplelithophil_ExclSchool = 100 * sum(N_TAXA[REPRO_SILI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TROPHIC
, pi_detritivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_DE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_gen_ExclSchool = 100 * sum(N_TAXA[TROPHIC_GE == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_herbivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_HB == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_insctCypr_ExclSchool = 100 * sum(N_TAXA[TROPHIC_IN_CYP == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
# , ni_insectivore_notoler_ExclSchool = sum(N_TAXA[TROPHIC_IN_noT == TRUE
# & TYPE_SCHOOL == FALSE]
# , na.rm = TRUE)
, pi_insectivore_notoler_ExclSchool = 100 * sum(N_TAXA[TROPHIC_IN_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_piscivore_ExclSchool = 100 * sum(N_TAXA[TROPHIC_PI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TOLER
, pi_tv_intol_ExclSchool = 100 * sum(N_TAXA[TOLER_I == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_intolcoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_ICW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_sens_ExclSchool = 100 * sum(N_TAXA[TOLER_S == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_senscoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_SCW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_toler_ExclSchool = 100 * sum(N_TAXA[TOLER_T == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_tv_tolercoldwater_ExclSchool = 100 * sum(N_TAXA[TOLER_TCW == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, TYPE
, pi_exotic_ExclSchool = 100 * sum(N_TAXA[TYPE_EX == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_minnow_notoler_ExclSchool = 100 * sum(N_TAXA[TYPE_MIN_noT == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_Perciformes_ExclSchool = 100 * sum(N_TAXA[TYPE_PERC == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_pioneer_ExclShool = 100 * sum(N_TAXA[TYPE_PI == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
, pi_shortlived_ExclSchool = 100 * sum(N_TAXA[TYPE_SL == TRUE
& TYPE_SCHOOL == FALSE]
, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pi, other
, pi_dom02_ExclSchool = 100 * max(ni_dom02_ExclSchool, na.rm = TRUE) / ni_total_ExclSchool
#### MN, pt, HABITAT
, pt_natcoldwater = 100 * nt_natcoldwater / nt_total
#### MN, pt, REPRO
, pt_serialspawner = 100 * nt_serialspawner / nt_total
, pt_simplelithophil = 100 * nt_simplelithophil / nt_total
#### MN, pt, TOLER
, pt_tv_sens = 100 * nt_tv_sens / nt_total
, pt_tv_senscoldwater = 100 * nt_tv_senscoldwater / nt_total
, pt_tv_toler = 100 * nt_tv_toler / nt_total
, pt_tv_vtoler = 100 * nt_tv_vtoler / nt_total
#### MN, pt, TROPHIC
, pt_beninsct_notoler = 100 * nt_beninsct_notoler / nt_total
, pt_detritivore = 100 * nt_detritivore / nt_total
, pt_gen = 100 * nt_gen / nt_total
, pt_insectivore_notoler = 100 * nt_insectivore_notoler / nt_total
, pt_omnivore = 100 * nt_omnivore / nt_total
#### MN, pt, TYPE
, pt_darterscultpinsucker = 100 * nt_darterscultpinsucker / nt_total
, pt_pioneer = 100 * nt_pioneer / nt_total
#### MN, x
, ni_m_notoler = ni_total_notoler_mn / length_m
#### MN, DELT
, pi_delt_ExclSchool = 100 * sum(N_ANOMALIES[TYPE_SCHOOL != TRUE]
, na.rm = TRUE) / ni_total_ExclSchool
#
# name changes ####
# # MBSS metric names
# , STRMAREA = area
# , TOTCNT = ni_total
# , ABUNSQM = ni_m2
# , PABDOM = pi_dom01
# , TOTBIOM = x_biomass_total
# , BIOM_MSQ = x_biomass_m2
# , NUMBENTSP = nt_benthic
# # , NUMBROOK = ni_brooktrout
# , PBROOK = pi_brooktrout
# # , NUMGEOMIV = ni_genomninvrt
# , PGEOMIV = pi_genomninvrt
# # , NUMIS = ni_insectivore
# , P_IS = pi_insectivore
# # , NUMLITH = ni_lithophil
# , P_LITH = pi_lithophil
# # , NUMROUND = ni_rbs
# , PROUND = pi_rbs
# # , NUMSCULP = ni_sculpin
# , PSCULP = pi_sculpin
# # , NUMTOL = ni_tv_toler
# , PTOL = pi_tv_toler
#
)## met.val.END
if (verbose == TRUE) {
# 7
debug_topic <- "clean up"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
#
# replace NA with 0
met.val[is.na(met.val)] <- 0
#
# # # subset to only metrics specified by user
# # if (!is.null(MetricNames)) {
# # met.val <- met.val[,c(Index_Name, SITE, INDEX_CLASS, ACREAGE, LEN_SAMP, MetricNames)]
# # }
# myFlds_Remove <- c("ni_total", "pi_rbs",
# , "pi_brooktrout", "pi_sculpin", "nt_total"
# , "nt_benthic", "pi_lithophil",
# , "pi_genomninvrt", "pi_insectivore",
# , "pi_tv_toler", "pi_dom01", "area", "ni_m2"
# , "x_biomass_total", "x_biomass_m2")
# met.val <- met.val[,-match(myFlds_Remove,names(met.val))]
# # subset to only metrics specified by user
if (verbose == TRUE) {
# 8
debug_topic <- "subset"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(MetricNames)) {
#met.val <- met.val
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (verbose == TRUE) {
# 9
debug_topic <- "extra fields"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>%
dplyr::group_by(.dots = c("SAMPLEID", cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val)
, by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# adjust ----
# #
# # Adjust metrics (MBSS always adjust so remove IF/THEN)
# # added as extra columns to output
# #if (boo.Adjust==TRUE) {##IF.boo.Ajust.START
# # MBSS.2005.Fish
# # nt_benthic
# met.val[,"NUMBENTSP_Obs"] <- met.val[,"NUMBENTSP"]
# # Expected constants
# ## m
# met.val[,"NUMBENTSP_m"] <- NA
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="COASTAL"] <- 1.69
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="EPIEDMONT"] <- 1.25
# met.val[,"NUMBENTSP_m"][met.val[,"INDEX_CLASS"]=="HIGHLAND"] <- 1.23
# ## b
# met.val[,"NUMBENTSP_b"] <- NA
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="COASTAL"] <- -3.33
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="EPIEDMONT"] <- -2.36
# met.val[,"NUMBENTSP_b"][met.val[,"INDEX_CLASS"]=="HIGHLAND"] <- -2.35
# # Calc Expected
# met.val[,"NUMBENTSP_Exp"] <- (met.val[,"NUMBENTSP_m"] * log10(met.val[,"ACREAGE"])) + met.val[,"NUMBENTSP_b"]
# # Calc Adjusted
# met.val[,"NUMBENTSP_Adj"] <- met.val[,"NUMBENTSP_Obs"] / met.val[,"NUMBENTSP_Exp"]
# # Rename base metric with adjusted value
# met.val[,"NUMBENTSP"] <- met.val[,"NUMBENTSP_Adj"]
# # NA to zero
# met.val[,"NUMBENTSP"][is.na(met.val[,"NUMBENTSP"])] <- 0
#
# #}##IF.boo.Ajust.END
#
# df to report back
if (verbose == TRUE) {
# 10
debug_topic <- "return results"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
return(df.return)
}##FUNCTION.metric.values.fish.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, Algae
#'
#' @description Subfunction of metric.values for use with Algae.
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.algae <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.Shiny = FALSE
, verbose) {
time_start <- Sys.time()
# global variable bindings ----
N_TAXA <- NULL
NONTARGET <- SAMPLEID <- INDEX_NAME <- INDEX_CLASS <- ni_total <- TAXAID <-
EXCLUDE <- GENUS <- LOW_N <- HIGH_N <- LOW_P <- HIGH_P <- BC_1 <- BC_2 <-
BC_3 <- BC_4 <- BC_5 <- PT_1 <- PT_2 <- PT_3 <- PT_4 <- PT_5 <-
SALINITY_1 <- SALINITY_2 <- SALINITY_3 <- SALINITY_4 <- O_1 <- O_2 <- O_3 <-
O_4 <- O_5 <- SESTONIC_HABIT <- BENTHIC_HABIT <- BAHLS_1 <- BAHLS_2 <-
BAHLS_3 <- TROPHIC_1 <- TROPHIC_2 <- TROPHIC_3 <- TROPHIC_4 <- TROPHIC_5 <-
TROPHIC_6 <- TROPHIC_7 <- SAP_1 <- SAP_2 <- SAP_3 <- SAP_4 <- SAP_5 <-
NON_N_FIXER <- N_FIXER <- HIGHLY_MOTILE <- MODERATELY_MOTILE <-
NON_MOTILE <- SLIGHTLY_MOTILE <- WEAKLY_MOTILE <- BIG <- SMALL <- MEDIUM <-
VERY_BIG <- VERY_SMALL <- ADNATE <- STALKED <- HIGHLY_MOTILE.1 <- ARAPHID <-
DIAT_CL <- BEN_SES <- DIAT_CA <- DIAT_COND <- DIATAS_TN <- DIATAS_TP <-
MOTILITY <- NF <- pi_DIAT_CL_1 <- nt_Achnan_Navic <- nt_total <-
nt_HIGH_N <- nt_LOW_N <- nt_HIGH_P <- nt_LOW_P <- nt_BC_1 <- nt_BC_2 <-
nt_BC_3 <- nt_BC_4 <- nt_BC_5 <- nt_BC_12 <- nt_BC_45 <- nt_PT_1 <-
nt_PT_2 <- nt_PT_3 <- nt_PT_4 <- nt_PT_5 <- nt_PT_12 <- nt_SALINITY_1 <-
nt_SALINITY_2 <- nt_SALINITY_3 <- nt_SALINITY_4 <- nt_SALINITY_34 <-
nt_O_1 <- nt_O_2 <- nt_O_3 <- nt_O_4 <- nt_O_5 <- nt_O_345 <-
nt_SESTONIC_HABIT <- nt_BENTHIC_HABIT <- nt_BAHLS_1 <- nt_BAHLS_2 <-
nt_BAHLS_3 <- nt_TROPHIC_1 <- nt_TROPHIC_2 <- nt_TROPHIC_3 <-
nt_TROPHIC_4 <- nt_TROPHIC_5 <- nt_TROPHIC_6 <- nt_TROPHIC_7 <-
nt_TROPHIC_456 <- nt_SAP_1 <- nt_SAP_2 <- nt_SAP_3 <- nt_SAP_4 <-
nt_SAP_5 <- nt_NON_N_FIXER <- nt_N_FIXER <- nt_HIGHLY_MOTILE <-
nt_MODERATELY_MOTILE <- nt_NON_MOTILE <- nt_SLIGHTLY_MOTILE <-
nt_WEAKLY_MOTILE <- nt_BIG <- nt_SMALL <- nt_MEDIUM <- nt_VERY_BIG <-
nt_VERY_SMALL <- nt_ADNATE <- nt_STALKED <- nt_HIGHLY_MOTILE.1 <-
nt_ARAPHID <- nt_DIAT_CL_1 <- nt_DIAT_CL_2 <- nt_BEN_SES_1 <-
nt_BEN_SES_2 <- nt_DIAT_CA_1 <- nt_DIAT_CA_2 <- nt_DIAT_COND_1 <-
nt_DIAT_COND_2 <- nt_DIATAS_TN_1 <- nt_DIATAS_TN_2 <- nt_DIATAS_TP_1 <-
nt_DIATAS_TP_2 <- nt_MOTILITY_1 <- nt_MOTILITY_2 <- nt_NF_1 <- nt_NF_2 <-
TOLVAL <- REF_INDICATORS <- nt_Sens_810 <- nt_RefIndicators <- nt_Tol_13 <-
POLL_TOL <- NULL
nt_TROPHIC_12 <- nt_TROPHIC_56 <- pi_BC_12 <- pt_TROPHIC_12 <-
pt_TROPHIC_56 <- NULL
# define pipe
`%>%` <- dplyr::`%>%`
# QC----
# QC, Required Fields
## QC, Missing Cols ----
# col.req_character <- c("SAMPLEID", "TAXAID", "INDEX_NAME", "INDEX_CLASS"
# , "PHYLUM", "ORDER", "FAMILY", "GENUS"
# )
# col.req_logical <- c("EXCLUDE", "NONTARGET")
# col.req_numeric <- c("N_TAXA")
# col.req <- c(col.req_character, col.req_logical, col.req_numeric)
col.req <- c("INDEX_NAME", "INDEX_CLASS", "SAMPLEID","TAXAID","N_TAXA"
,"EXCLUDE","NONTARGET"
,"PHYLUM","ORDER","FAMILY","GENUS","BC_USGS"
,"TROPHIC_USGS","SAP_USGS","PT_USGS","O_USGS","SALINITY_USGS"
,"BAHLS_USGS","P_USGS","N_USGS","HABITAT_USGS","N_FIXER_USGS"
,"MOTILITY_USGS","SIZE_USGS","HABIT_USGS","MOTILE2_USGS"
,"TOLVAL","DIATOM_ISA","DIAT_CL","POLL_TOL","BEN_SES"
,"DIATAS_TP","DIATAS_TN","DIAT_COND","DIAT_CA","MOTILITY"
,"NF")
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {##IF.num.col.req.missing.START
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the HABIT field is missing all habit related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" ", myPrompt.01, myPrompt.02, " ", myPrompt.03, myPrompt.04
, myPrompt.05, sep = "\n")
#user.input <- readline(prompt=myPrompt)
user.input <- NA
# special condition for Shiny
#Shiny counts as interactive()==TRUE but cannot access this prompt in Shiny.
if (boo.Shiny == FALSE) {
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ boo.Shiny ~ END
# any answer other than "YES" will stop the function.
if (user.input != 1) {##IF.user.input.START
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
myDF[,col.req.missing] <- NA
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.num.col.req.missing.END
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, Exclude ----
# as TRUE/FALSE
Exclude.T <- sum(myDF$EXCLUDE == TRUE, na.rm = TRUE)
if (Exclude.T == 0) {##IF.Exclude.T.START
warning("EXCLUDE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, NonTarget ----
# as TRUE/FALSE
NonTarget.F <- sum(myDF$NONTARGET == FALSE, na.rm = TRUE)
if (NonTarget.F == 0) {##IF.Exclude.T.START
warning("NONTARGET column does not have any FALSE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.Exclude.T.END
## QC, TolVal----
# need as numeric, if have "NA" as character it fails
TolVal_Char_NA <- myDF[, "TOLVAL"] == "NA"
if (sum(TolVal_Char_NA, na.rm = TRUE) > 0) {
myDF[TolVal_Char_NA, "TOLVAL"] <- NA
myDF[, "TOLVAL"] <- as.numeric(myDF[, "TOLVAL"])
}##IF ~ TOLVAL ~ END
# Data Munging----
# Remove NonTarget Taxa (added back 20200715, missing since 20200224)
# Function fails if all NA (e.g., column was missing) (20200724)
myDF <- myDF %>% dplyr::filter(NONTARGET != TRUE | is.na(NONTARGET))
# Convert values to upper case (FFG, Habit, Life_Cycle)
myDF[, "BC_USGS"] <- toupper(myDF[, "BC_USGS"])
myDF[, "PT_USGS"] <- toupper(myDF[, "PT_USGS"])
myDF[, "O_USGS"] <- toupper(myDF[, "O_USGS"])
myDF[, "SALINITY_USGS"] <- toupper(myDF[, "SALINITY_USGS"])
myDF[, "P_USGS"] <- toupper(myDF[, "P_USGS"])
myDF[, "N_USGS"] <- toupper(myDF[, "N_USGS"])
myDF[, "HABITAT_USGS"] <- toupper(myDF[, "HABITAT_USGS"])
myDF[, "BAHLS_USGS"] <- toupper(myDF[, "BAHLS_USGS"])
myDF[, "TROPHIC_USGS"] <- toupper(myDF[, "TROPHIC_USGS"])
myDF[, "DIATOM_ISA"] <- toupper(myDF[, "DIATOM_ISA"])
myDF[, "SAP_USGS"] <- toupper(myDF[, "SAP_USGS"])
myDF[, "N_FIXER_USGS"] <- toupper(myDF[, "N_FIXER_USGS"])
myDF[, "MOTILITY_USGS"] <- toupper(myDF[, "MOTILITY_USGS"])
myDF[, "SIZE_USGS"] <- toupper(myDF[, "SIZE_USGS"])
myDF[, "HABIT_USGS"] <- toupper(myDF[, "HABIT_USGS"])
myDF[, "MOTILE2_USGS"] <- toupper(myDF[, "MOTILE2_USGS"])
myDF[, "DIATOM_ISA"] <- toupper(myDF[, "DIATOM_ISA"])
# Add extra columns for some fields
# (need unique values for functions in summarise)
# each will be TRUE or FALSE
# finds any match so "CN, CB" is both "CN" and "CB"
myDF[, "BC_1"] <- grepl("BC_1", myDF[, "BC_USGS"])
myDF[, "BC_2"] <- grepl("BC_2", myDF[, "BC_USGS"])
myDF[, "BC_3"] <- grepl("BC_3", myDF[, "BC_USGS"])
myDF[, "BC_4"] <- grepl("BC_4", myDF[, "BC_USGS"])
myDF[, "BC_5"] <- grepl("BC_5", myDF[, "BC_USGS"])
myDF[, "PT_1"] <- grepl("PT_1", myDF[, "PT_USGS"])
myDF[, "PT_2"] <- grepl("PT_2", myDF[, "PT_USGS"])
myDF[, "PT_3"] <- grepl("PT_3", myDF[, "PT_USGS"])
myDF[, "PT_4"] <- grepl("PT_4", myDF[, "PT_USGS"])
myDF[, "PT_5"] <- grepl("PT_5", myDF[, "PT_USGS"])
myDF[, "O_1"] <- grepl("O_1", myDF[, "O_USGS"])
myDF[, "O_2"] <- grepl("O_2", myDF[, "O_USGS"])
myDF[, "O_3"] <- grepl("O_3", myDF[, "O_USGS"])
myDF[, "O_4"] <- grepl("O_4", myDF[, "O_USGS"])
myDF[, "O_5"] <- grepl("O_5", myDF[, "O_USGS"])
myDF[, "SALINITY_1"] <- grepl("SALINITY_1", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_2"] <- grepl("SALINITY_2", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_3"] <- grepl("SALINITY_3", myDF[, "SALINITY_USGS"])
myDF[, "SALINITY_4"] <- grepl("SALINITY_4", myDF[, "SALINITY_USGS"])
myDF[, "HIGH_P"] <- grepl("HIGH_P", myDF[, "P_USGS"])
myDF[, "LOW_P"] <- grepl("LOW_P", myDF[, "P_USGS"])
myDF[, "HIGH_N"] <- grepl("HIGH_N", myDF[, "N_USGS"])
myDF[, "LOW_N"] <- grepl("LOW_N", myDF[, "N_USGS"])
myDF[, "BENTHIC_HABIT"] <- grepl("BENTHIC_HABIT", myDF[, "HABITAT_USGS"])
myDF[, "SESTONIC_HABIT"] <- grepl("SESTONIC_HABIT", myDF[, "HABITAT_USGS"])
myDF[, "BAHLS_1"] <- grepl("BAHLS_1", myDF[, "BAHLS_USGS"])
myDF[, "BAHLS_2"] <- grepl("BAHLS_2", myDF[, "BAHLS_USGS"])
myDF[, "BAHLS_3"] <- grepl("BAHLS_3", myDF[, "BAHLS_USGS"])
myDF[, "TROPHIC_1"] <- grepl("TROPHIC_1", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_2"] <- grepl("TROPHIC_2", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_3"] <- grepl("TROPHIC_3", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_4"] <- grepl("TROPHIC_4", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_5"] <- grepl("TROPHIC_5", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_6"] <- grepl("TROPHIC_6", myDF[, "TROPHIC_USGS"])
myDF[, "TROPHIC_7"] <- grepl("TROPHIC_7", myDF[, "TROPHIC_USGS"])
myDF[, "SAP_1"] <- grepl("SAP_1", myDF[, "SAP_USGS"])
myDF[, "SAP_2"] <- grepl("SAP_2", myDF[, "SAP_USGS"])
myDF[, "SAP_3"] <- grepl("SAP_3", myDF[, "SAP_USGS"])
myDF[, "SAP_4"] <- grepl("SAP_4", myDF[, "SAP_USGS"])
myDF[, "SAP_5"] <- grepl("SAP_5", myDF[, "SAP_USGS"])
myDF[, "NON_N_FIXER"] <- grepl("NON_N_FIXER", myDF[, "N_FIXER_USGS"])
myDF[, "N_FIXER"] <- grepl("\\bN_FIXER\\b", myDF[, "N_FIXER_USGS"])
myDF[, "HIGHLY_MOTILE"] <- grepl("HIGHLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "MODERATELY_MOTILE"] <- grepl("MODERATELY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "NON_MOTILE"] <- grepl("NON_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "SLIGHTLY_MOTILE"] <- grepl("SLIGHTLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "WEAKLY_MOTILE"] <- grepl("WEAKLY_MOTILE", myDF[, "MOTILITY_USGS"])
myDF[, "BIG"] <- grepl("\\bBIG\\b", myDF[, "SIZE_USGS"])
myDF[, "MEDIUM"] <- grepl("MEDIUM", myDF[, "SIZE_USGS"])
myDF[, "SMALL"] <- grepl("\\bSMALL\\b", myDF[, "SIZE_USGS"])
myDF[, "VERY_BIG"] <- grepl("VERY_BIG", myDF[, "SIZE_USGS"])
myDF[, "VERY_SMALL"] <- grepl("VERY_SMALL", myDF[, "SIZE_USGS"])
myDF[, "ADNATE"] <- grepl("ADNATE", myDF[, "HABIT_USGS"])
myDF[, "STALKED"] <- grepl("STALKED", myDF[, "HABIT_USGS"])
myDF[, "HIGHLY_MOTILE.1"] <- grepl("HIGHLY_MOTILE.1", myDF[, "MOTILE2_USGS"])
myDF[, "ARAPHID"] <- grepl("ARAPHID", myDF[, "MOTILE2_USGS"])
myDF[, "REF_INDICATORS"] <- grepl("^REF", myDF[, "DIATOM_ISA"])
# Metric Calc----
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF, SAMPLEID, INDEX_NAME
, INDEX_CLASS)
#
## Individuals ----
, ni_total = sum(N_TAXA, na.rm = TRUE)
, li_total = log(ni_total)
## Number of Taxa ----
, nt_total = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_TAXA > 0]
, na.rm = TRUE)
### Phylo----
, nt_Achnan_Navic = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (GENUS == "Achnanthidium"
| GENUS == "Navicula")]
, na.rm = TRUE)
### N_USGS----
, nt_LOW_N = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LOW_N == TRUE]
, na.rm = TRUE)
, nt_HIGH_N = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGH_N == TRUE]
, na.rm = TRUE)
### P_USGS----
, nt_LOW_P = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& LOW_P == TRUE]
, na.rm = TRUE)
, nt_HIGH_P = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGH_P == TRUE]
, na.rm = TRUE)
### BC_USGS----
, nt_BC_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_1 == TRUE]
, na.rm = TRUE)
, nt_BC_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_2 == TRUE]
, na.rm = TRUE)
, nt_BC_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_3 == TRUE]
, na.rm = TRUE)
, nt_BC_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_4 == TRUE]
, na.rm = TRUE)
, nt_BC_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BC_5 == TRUE]
, na.rm = TRUE)
, nt_BC_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BC_1 == TRUE
| BC_2 == TRUE)]
, na.rm = TRUE)
, nt_BC_45 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BC_4 == TRUE
| BC_5 == TRUE)]
, na.rm = TRUE)
### PT_USGS----
, nt_PT_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_1 == TRUE]
, na.rm = TRUE)
, nt_PT_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_2 == TRUE]
, na.rm = TRUE)
, nt_PT_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_3 == TRUE]
, na.rm = TRUE)
, nt_PT_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_4 == TRUE]
, na.rm = TRUE)
, nt_PT_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& PT_5 == TRUE]
, na.rm = TRUE)
, nt_PT_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (PT_1 == TRUE
| PT_2 == TRUE)]
, na.rm = TRUE)
### SALINITY_USGS----
, nt_SALINITY_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_1 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_2 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_3 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SALINITY_4 == TRUE]
, na.rm = TRUE)
, nt_SALINITY_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (SALINITY_1 == TRUE
| SALINITY_2 == TRUE)]
, na.rm = TRUE)
, nt_SALINITY_34 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (SALINITY_3 == TRUE
| SALINITY_4 == TRUE)]
, na.rm = TRUE)
### O_USGS----
, nt_O_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_1 == TRUE]
, na.rm = TRUE)
, nt_O_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_2 == TRUE]
, na.rm = TRUE)
, nt_O_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_3 == TRUE]
, na.rm = TRUE)
, nt_O_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_4 == TRUE]
, na.rm = TRUE)
, nt_O_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& O_5 == TRUE]
, na.rm = TRUE)
, nt_O_345 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (O_3 == TRUE
| O_4 == TRUE
| O_5 == TRUE)]
, na.rm = TRUE)
### HABITAT_USGS----
, nt_SESTONIC_HABIT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SESTONIC_HABIT == TRUE]
, na.rm = TRUE)
, nt_BENTHIC_HABIT = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BENTHIC_HABIT == TRUE]
, na.rm = TRUE)
### BAHLS_USGS----
, nt_BAHLS_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_1 == TRUE)]
, na.rm = TRUE)
, nt_BAHLS_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_2 == TRUE)]
, na.rm = TRUE)
, nt_BAHLS_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (BAHLS_3 == TRUE)]
, na.rm = TRUE)
### TROPHIC_USGS----
, nt_TROPHIC_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_1 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_2 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_3 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_4 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_5 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_6 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_6 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_7 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TROPHIC_7 == TRUE]
, na.rm = TRUE)
, nt_TROPHIC_12 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_1 == TRUE
| TROPHIC_2 == TRUE)]
, na.rm = TRUE)
, nt_TROPHIC_456 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_4 == TRUE
| TROPHIC_5 == TRUE
| TROPHIC_6 == TRUE)]
, na.rm = TRUE)
, nt_TROPHIC_56 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& (TROPHIC_5 == TRUE
| TROPHIC_6 == TRUE)]
, na.rm = TRUE)
### SAP_USGS----
, nt_SAP_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_1 == TRUE]
, na.rm = TRUE)
, nt_SAP_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_2 == TRUE]
, na.rm = TRUE)
, nt_SAP_3 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_3 == TRUE]
, na.rm = TRUE)
, nt_SAP_4 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_4 == TRUE]
, na.rm = TRUE)
, nt_SAP_5 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SAP_5 == TRUE]
, na.rm = TRUE)
### N_FIXER_USGS----
, nt_NON_N_FIXER = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NON_N_FIXER == TRUE]
, na.rm = TRUE)
, nt_N_FIXER = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& N_FIXER == TRUE]
, na.rm = TRUE)
### MOTILITY_USGS----
, nt_HIGHLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGHLY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_MODERATELY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MODERATELY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_NON_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NON_MOTILE == TRUE]
, na.rm = TRUE)
, nt_SLIGHTLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SLIGHTLY_MOTILE == TRUE]
, na.rm = TRUE)
, nt_WEAKLY_MOTILE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& WEAKLY_MOTILE == TRUE]
, na.rm = TRUE)
### SIZE_USGS----
, nt_BIG = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BIG == TRUE]
, na.rm = TRUE)
, nt_SMALL = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& SMALL == TRUE]
, na.rm = TRUE)
, nt_MEDIUM = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MEDIUM == TRUE]
, na.rm = TRUE)
, nt_VERY_BIG = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& VERY_BIG == TRUE]
, na.rm = TRUE)
, nt_VERY_SMALL = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& VERY_SMALL == TRUE]
, na.rm = TRUE)
### HABIT_USGS----
, nt_ADNATE = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ADNATE == TRUE]
, na.rm = TRUE)
, nt_STALKED = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& STALKED == TRUE]
, na.rm = TRUE)
### MOTILE2_USGS----
, nt_HIGHLY_MOTILE.1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& HIGHLY_MOTILE.1 == TRUE]
, na.rm = TRUE)
, nt_ARAPHID = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& ARAPHID == TRUE]
, na.rm = TRUE)
### DIAT_CL----
, nt_DIAT_CL_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CL == 1]
, na.rm = TRUE)
, nt_DIAT_CL_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CL == 2]
, na.rm = TRUE)
### BEN_SES----
, nt_BEN_SES_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BEN_SES == 1]
, na.rm = TRUE)
, nt_BEN_SES_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& BEN_SES == 2]
, na.rm = TRUE)
### DIAT_CA----
, nt_DIAT_CA_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CA == 1]
, na.rm = TRUE)
, nt_DIAT_CA_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_CA == 2]
, na.rm = TRUE)
### DIAT_COND----
, nt_DIAT_COND_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_COND == 1]
, na.rm = TRUE)
, nt_DIAT_COND_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIAT_COND == 2]
, na.rm = TRUE)
### DIATAS----
, nt_DIATAS_TN_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TN == 1]
, na.rm = TRUE)
, nt_DIATAS_TN_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TN == 2]
, na.rm = TRUE)
, nt_DIATAS_TP_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TP == 1]
, na.rm = TRUE)
, nt_DIATAS_TP_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& DIATAS_TP == 2]
, na.rm = TRUE)
### MOTILITY----
, nt_MOTILITY_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MOTILITY == 1]
, na.rm = TRUE)
, nt_MOTILITY_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& MOTILITY == 2]
, na.rm = TRUE)
### NF----
, nt_NF_1 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NF == 1]
, na.rm = TRUE)
, nt_NF_2 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& NF == 2]
, na.rm = TRUE)
## Percent Individuals----
### Phylo----
, pi_Achnan_Navic = 100 * sum(N_TAXA[GENUS == "Achnanthidium"
| GENUS == "Navicula"]
, na.rm = TRUE) / ni_total
### N_USGS---
, pi_HIGH_N = 100 * sum(N_TAXA[HIGH_N == TRUE]
, na.rm = TRUE) / ni_total
, pi_LOW_N = 100 * sum(N_TAXA[LOW_N == TRUE]
, na.rm = TRUE) / ni_total
### P_USGS---
, pi_HIGH_P = 100 * sum(N_TAXA[HIGH_P == TRUE]
, na.rm = TRUE) / ni_total
, pi_LOW_P = 100 * sum(N_TAXA[LOW_P == TRUE]
, na.rm = TRUE) / ni_total
### BC_USGS---
, pi_BC_1 = 100 * sum(N_TAXA[BC_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_2 = 100 * sum(N_TAXA[BC_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_3 = 100 * sum(N_TAXA[BC_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_4 = 100 * sum(N_TAXA[BC_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_5 = 100 * sum(N_TAXA[BC_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BC_12 = 100 * sum(N_TAXA[BC_1 == TRUE
| BC_2 == TRUE]
, na.rm = TRUE) / ni_total
### PT_USGS---
, pi_PT_1 = 100 * sum(N_TAXA[PT_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_2 = 100 * sum(N_TAXA[PT_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_3 = 100 * sum(N_TAXA[PT_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_4 = 100 * sum(N_TAXA[PT_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_5 = 100 * sum(N_TAXA[PT_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_PT_45 = 100 * sum(N_TAXA[PT_4 == TRUE
| PT_5 == TRUE]
, na.rm = TRUE) / ni_total
### SALINITY_USGS---
, pi_SALINITY_1 = 100 * sum(N_TAXA[SALINITY_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_2 = 100 * sum(N_TAXA[SALINITY_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_3 = 100 * sum(N_TAXA[SALINITY_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SALINITY_4 = 100 * sum(N_TAXA[SALINITY_4 == TRUE]
, na.rm = TRUE) / ni_total
### O_USGS---
, pi_O_1 = 100 * sum(N_TAXA[O_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_2 = 100 * sum(N_TAXA[O_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_3 = 100 * sum(N_TAXA[O_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_4 = 100 * sum(N_TAXA[O_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_O_5 = 100 * sum(N_TAXA[O_5 == TRUE]
, na.rm = TRUE) / ni_total
### HABITAT_USGS---
, pi_SESTONIC_HABIT = 100 * sum(N_TAXA[SESTONIC_HABIT == TRUE]
, na.rm = TRUE) / ni_total
, pi_BENTHIC_HABIT = 100 * sum(N_TAXA[BENTHIC_HABIT == TRUE]
, na.rm = TRUE) / ni_total
### BAHLS_USGS---
, pi_BAHLS_1 = 100 * sum(N_TAXA[BAHLS_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BAHLS_2 = 100 * sum(N_TAXA[BAHLS_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_BAHLS_3 = 100 * sum(N_TAXA[BAHLS_3 == TRUE]
, na.rm = TRUE) / ni_total
### TROPHIC_USGS---
, pi_TROPHIC_1 = 100 * sum(N_TAXA[TROPHIC_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_2 = 100 * sum(N_TAXA[TROPHIC_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_3 = 100 * sum(N_TAXA[TROPHIC_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_4 = 100 * sum(N_TAXA[TROPHIC_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_5 = 100 * sum(N_TAXA[TROPHIC_5 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_6 = 100 * sum(N_TAXA[TROPHIC_6 == TRUE]
, na.rm = TRUE) / ni_total
, pi_TROPHIC_7 = 100 * sum(N_TAXA[TROPHIC_7 == TRUE]
, na.rm = TRUE) / ni_total
### SAP_USGS----
, pi_SAP_1 = 100 * sum(N_TAXA[SAP_1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_2 = 100 * sum(N_TAXA[SAP_2 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_3 = 100 * sum(N_TAXA[SAP_3 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_4 = 100 * sum(N_TAXA[SAP_4 == TRUE]
, na.rm = TRUE) / ni_total
, pi_SAP_5 = 100 * sum(N_TAXA[SAP_5 == TRUE]
, na.rm = TRUE) / ni_total
### N_FIXER_USGS----
, pi_NON_N_FIXER = 100 * sum(N_TAXA[NON_N_FIXER == TRUE]
, na.rm = TRUE) / ni_total
, pi_N_FIXER = 100 * sum(N_TAXA[N_FIXER == TRUE]
, na.rm = TRUE) / ni_total
### MOTILITY_USGS----
, pi_HIGHLY_MOTILE = 100 * sum(N_TAXA[HIGHLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_MODERATELY_MOTILE = 100 * sum(N_TAXA[MODERATELY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_NON_MOTILE = 100 * sum(N_TAXA[NON_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_SLIGHTLY_MOTILE = 100 * sum(N_TAXA[SLIGHTLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
, pi_WEAKLY_MOTILE = 100 * sum(N_TAXA[WEAKLY_MOTILE == TRUE]
, na.rm = TRUE) / ni_total
### SIZE_USGS----
, pi_BIG = 100 * sum(N_TAXA[BIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_SMALL = 100 * sum(N_TAXA[SMALL == TRUE]
, na.rm = TRUE) / ni_total
, pi_MEDIUM = 100 * sum(N_TAXA[MEDIUM == TRUE]
, na.rm = TRUE) / ni_total
, pi_VERY_BIG = 100 * sum(N_TAXA[VERY_BIG == TRUE]
, na.rm = TRUE) / ni_total
, pi_VERY_SMALL = 100 * sum(N_TAXA[VERY_SMALL == TRUE]
, na.rm = TRUE) / ni_total
### HABIT_USGS----
, pi_ADNATE = 100 * sum(N_TAXA[ADNATE == TRUE]
, na.rm = TRUE) / ni_total
, pi_STALKED = 100 * sum(N_TAXA[STALKED == TRUE]
, na.rm = TRUE) / ni_total
### MOTILE2_USGS----
, pi_HIGHLY_MOTILE.1 = 100 * sum(N_TAXA[HIGHLY_MOTILE.1 == TRUE]
, na.rm = TRUE) / ni_total
, pi_ARAPHID = 100 * sum(N_TAXA[ARAPHID == TRUE]
, na.rm = TRUE) / ni_total
### DIAT_CL----
, pi_DIAT_CL_1 = 100 * sum(N_TAXA[DIAT_CL == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_CL_1_ASSR = 100 * (asin(sqrt(pi_DIAT_CL_1 / 100)))
, pi_DIAT_CL_2 = 100 * sum(N_TAXA[DIAT_CL == 2]
, na.rm = TRUE) / ni_total
### BEN_SES----
, pi_BEN_SES_1 = 100 * sum(N_TAXA[BEN_SES == 1]
, na.rm = TRUE) / ni_total
, pi_BEN_SES_2 = 100 * sum(N_TAXA[BEN_SES == 2]
, na.rm = TRUE) / ni_total
### DIAT_CA----
, pi_DIAT_CA_1 = 100 * sum(N_TAXA[DIAT_CA == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_CA_2 = 100 * sum(N_TAXA[DIAT_CA == 2]
, na.rm = TRUE) / ni_total
### DIAT_COND----
, pi_DIAT_COND_1 = 100 * sum(N_TAXA[DIAT_COND == 1]
, na.rm = TRUE) / ni_total
, pi_DIAT_COND_2 = 100 * sum(N_TAXA[DIAT_COND == 2]
, na.rm = TRUE) / ni_total
### DIATAS----
, pi_DIATAS_TN_1 = 100 * sum(N_TAXA[DIATAS_TN == 1]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TN_2 = 100 * sum(N_TAXA[DIATAS_TN == 2]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TP_1 = 100 * sum(N_TAXA[DIATAS_TP == 1]
, na.rm = TRUE) / ni_total
, pi_DIATAS_TP_2 = 100 * sum(N_TAXA[DIATAS_TP == 2]
, na.rm = TRUE) / ni_total
### MOTILITY----
, pi_MOTILITY_1 = 100 * sum(N_TAXA[MOTILITY == 1]
, na.rm = TRUE) / ni_total
, pi_MOTILITY_2 = 100 * sum(N_TAXA[MOTILITY == 2]
, na.rm = TRUE) / ni_total
### NF----
, pi_NF_1 = 100 * sum(N_TAXA[NF == 1]
, na.rm = TRUE) / ni_total
, pi_NF_2 = 100 * sum(N_TAXA[NF == 2]
, na.rm = TRUE) / ni_total
## Percent of Taxa----
### Phylo----
, pt_Achnan_Navic = 100 * nt_Achnan_Navic / nt_total
### N_USGS----
, pt_HIGH_N = 100 * nt_HIGH_N / nt_total
, pt_LOW_N = 100 * nt_LOW_N / nt_total
### P_USGS----
, pt_HIGH_P = 100 * nt_HIGH_P / nt_total
, pt_LOW_P = 100 * nt_LOW_P / nt_total
### BC_USGS----
, pt_BC_1 = 100 * nt_BC_1 / nt_total
, pt_BC_2 = 100 * nt_BC_2 / nt_total
, pt_BC_3 = 100 * nt_BC_3 / nt_total
, pt_BC_4 = 100 * nt_BC_4 / nt_total
, pt_BC_5 = 100 * nt_BC_5 / nt_total
, pt_BC_12 = 100 * nt_BC_12 / nt_total
, pt_BC_12_adj = NA_real_
, pt_BC_45 = 100 * nt_BC_45 / nt_total
### PT_USGS----
, pt_PT_1 = 100 * nt_PT_1 / nt_total
, pt_PT_2 = 100 * nt_PT_2 / nt_total
, pt_PT_3 = 100 * nt_PT_3 / nt_total
, pt_PT_4 = 100 * nt_PT_4 / nt_total
, pt_PT_5 = 100 * nt_PT_5 / nt_total
, pt_PT_12 = 100 * nt_PT_12 / nt_total
### SALINITY_USGS----
, pt_SALINITY_1 = 100 * nt_SALINITY_1 / nt_total
, pt_SALINITY_2 = 100 * nt_SALINITY_2 / nt_total
, pt_SALINITY_3 = 100 * nt_SALINITY_3 / nt_total
, pt_SALINITY_4 = 100 * nt_SALINITY_4 / nt_total
, pt_SALINITY_34 = 100 * nt_SALINITY_34 / nt_total
### O_USGS----
, pt_O_1 = 100 * nt_O_1 / nt_total
, pt_O_2 = 100 * nt_O_2 / nt_total
, pt_O_3 = 100 * nt_O_3 / nt_total
, pt_O_4 = 100 * nt_O_4 / nt_total
, pt_O_5 = 100 * nt_O_5 / nt_total
, pt_O_345 = 100 * nt_O_345 / nt_total
### HABITAT_USGS----
, pt_SESTONIC_HABIT = 100 * nt_SESTONIC_HABIT / nt_total
, pt_BENTHIC_HABIT = 100 * nt_BENTHIC_HABIT / nt_total
### BAHLS_USGS----
, pt_BAHLS_1 = 100 * nt_BAHLS_1 / nt_total
, pt_BAHLS_2 = 100 * nt_BAHLS_2 / nt_total
, pt_BAHLS_3 = 100 * nt_BAHLS_3 / nt_total
### TROPHIC_USGS----
, pt_TROPHIC_1 = 100 * nt_TROPHIC_1 / nt_total
, pt_TROPHIC_2 = 100 * nt_TROPHIC_2 / nt_total
, pt_TROPHIC_3 = 100 * nt_TROPHIC_3 / nt_total
, pt_TROPHIC_4 = 100 * nt_TROPHIC_4 / nt_total
, pt_TROPHIC_5 = 100 * nt_TROPHIC_5 / nt_total
, pt_TROPHIC_6 = 100 * nt_TROPHIC_6 / nt_total
, pt_TROPHIC_7 = 100 * nt_TROPHIC_7 / nt_total
, pt_TROPHIC_12 = 100 * nt_TROPHIC_12 / nt_total
, pt_TROPHIC_456 = 100 * nt_TROPHIC_456 / nt_total
, pt_TROPHIC_56 = 100 * nt_TROPHIC_56 / nt_total
### SAP_USGS----
, pt_SAP_1 = 100 * nt_SAP_1 / nt_total
, pt_SAP_2 = 100 * nt_SAP_2 / nt_total
, pt_SAP_3 = 100 * nt_SAP_3 / nt_total
, pt_SAP_4 = 100 * nt_SAP_4 / nt_total
, pt_SAP_5 = 100 * nt_SAP_5 / nt_total
### N_FIXER_USGS----
, pt_NON_N_FIXER = 100 * nt_NON_N_FIXER / nt_total
, pt_N_FIXER = 100 * nt_N_FIXER / nt_total
### MOTILITY_USGS----
, pt_HIGHLY_MOTILE = 100 * nt_HIGHLY_MOTILE / nt_total
, pt_MODERATELY_MOTILE = 100 * nt_MODERATELY_MOTILE / nt_total
, pt_NON_MOTILE = 100 * nt_NON_MOTILE / nt_total
, pt_SLIGHTLY_MOTILE = 100 * nt_SLIGHTLY_MOTILE / nt_total
, pt_WEAKLY_MOTILE = 100 * nt_WEAKLY_MOTILE / nt_total
### SIZE_USGS----
, pt_BIG = 100 * nt_BIG / nt_total
, pt_SMALL = 100 * nt_SMALL / nt_total
, pt_MEDIUM = 100 * nt_MEDIUM / nt_total
, pt_VERY_BIG = 100 * nt_VERY_BIG / nt_total
, pt_VERY_SMALL = 100 * nt_VERY_SMALL / nt_total
### HABIT_USGS----
, pt_ADNATE = 100 * nt_ADNATE / nt_total
, pt_STALKED = 100 * nt_STALKED / nt_total
### MOTILE2_USGS----
, pt_HIGHLY_MOTILE.1 = 100 * nt_HIGHLY_MOTILE.1 / nt_total
, pt_ARAPHID = 100 * nt_ARAPHID / nt_total
### DIAT_CL----
, pt_DIAT_CL_1 = 100 * nt_DIAT_CL_1 / nt_total
, pt_DIAT_CL_2 = 100 * nt_DIAT_CL_2 / nt_total
### BEN_SES----
, pt_BEN_SES_1 = 100 * nt_BEN_SES_1 / nt_total
, pt_BEN_SES_2 = 100 * nt_BEN_SES_2 / nt_total
### DIAT_CA----
, pt_DIAT_CA_1 = 100 * nt_DIAT_CA_1 / nt_total
, pt_DIAT_CA_2 = 100 * nt_DIAT_CA_2 / nt_total
### DIAT_COND----
, pt_DIAT_COND_1 = 100 * nt_DIAT_COND_1 / nt_total
, pt_DIAT_COND_2 = 100 * nt_DIAT_COND_2 / nt_total
### DIATAS----
, pt_DIATAS_TN_1 = 100 * nt_DIATAS_TN_1 / nt_total
, pt_DIATAS_TN_2 = 100 * nt_DIATAS_TN_2 / nt_total
, pt_DIATAS_TP_1 = 100 * nt_DIATAS_TP_1 / nt_total
, pt_DIATAS_TP_2 = 100 * nt_DIATAS_TP_2 / nt_total
### MOTILITY----
, pt_MOTILITY_1 = 100 * nt_MOTILITY_1 / nt_total
, pt_MOTILITY_2 = 100 * nt_MOTILITY_2 / nt_total
### NF----
, pt_NF_1 = 100 * nt_NF_1 / nt_total
, pt_NF_2 = 100 * nt_NF_2 / nt_total
## Tolerance----
### Number of Taxa----
, nt_Sens_810 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE# DOES NOT FOLLOW NORMAL TOLVAL CONVENTION
& TOLVAL >= 8 # LOWER VALUES MORE TOLERANT (Indiana)
& TOLVAL <= 10]
, na.rm = TRUE)
, nt_RefIndicators = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE # Diatom Indicator Species Analysis
& REF_INDICATORS == TRUE]
, na.rm = TRUE)
, nt_Tol_13 = dplyr::n_distinct(TAXAID[EXCLUDE != TRUE
& TOLVAL >= 1# DOES NOT FOLLOW NORMAL TOLVAL CONVENTION
& TOLVAL <= 3]# LOWER VALUES MORE TOLERANT (Indiana)
, na.rm = TRUE)
### Percent of Individuals----
, pi_Sens_810 = 100 * sum(N_TAXA[TOLVAL >= 8
& TOLVAL <= 10]
, na.rm = TRUE) / sum(
N_TAXA[!is.na(TOLVAL)], na.rm = TRUE)
, pi_RefIndicators = 100 * sum(N_TAXA[REF_INDICATORS == TRUE], # Diatom Indicator Species Analysis
na.rm = TRUE) / ni_total
, pi_Tol_13 = 100 * sum(N_TAXA[TOLVAL >= 1 # DOES NOT FOLLOW NORMAL TOLVAL CONVENTION (Indiana)
& TOLVAL <= 3], na.rm = TRUE) / sum(
N_TAXA[!is.na(TOLVAL)], na.rm = TRUE) # LOWER VALUES MORE TOLERANT
### Percent of Taxa----
, pt_Sens_810 = 100 * nt_Sens_810 / nt_total # DOES NOT FOLLOW NORMAL TOLVAL CONVENTION (Indiana)
, pt_RefIndicators = 100 * nt_RefIndicators / nt_total
, pt_Tol_13 = 100 * nt_Tol_13 / nt_total
### Weighted Average ----
, wa_POLL_TOL = sum(N_TAXA[!is.na(POLL_TOL)]
* POLL_TOL[!is.na(POLL_TOL)
]) / sum(N_TAXA[!is.na(POLL_TOL)])
, .groups = "drop_last")##met.val.END
# Clean Up ####
# replace NA with 0
met.val[is.na(met.val)] <- 0
# subset to only metrics specified by user
if (is.null(MetricNames)) {
met.val <- met.val
} else {
met2include <- MetricNames[!(MetricNames %in% "ni_total")]
# remove ni_total if included as will always include it
met.val <- met.val[, c("SAMPLEID", "INDEX_CLASS", "INDEX_NAME",
"ni_total", met2include)]
}##IF~MetricNames~END
# Add extra fields
if (is.null(cols2keep)) {##IF.is.null.cols2keep.START
df.return <- as.data.frame(met.val)
} else {
# create df with grouped fields
myDF.cols2keep <- myDF %>% dplyr::group_by(.dots = c("SAMPLEID"
, cols2keep)) %>%
dplyr::summarize(col.drop = sum(N_TAXA))
col.drop <- ncol(myDF.cols2keep)
myDF.cols2keep <- myDF.cols2keep[,-col.drop]
# merge
df.return <- merge(as.data.frame(myDF.cols2keep)
, as.data.frame(met.val), by = "SAMPLEID")
}##IF.is.null.cols2keep.END
# Run Time
if (verbose) {
time_end <- Sys.time()
msg <- difftime(time_end, time_start)
message(msg)
}## IF ~ verbose
# df to report back
return(df.return)
}##FUNCTION.metric.values.algae.END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Calculate metric values, coral
#'
#' @description Subfunction of metric.values for use with coral
#'
#' @details For internal use only. Called from metric.values().
#'
#' @param myDF Data frame of taxa.
#' @param MetricNames Optional vector of metric names to be returned.
#' @param boo.Adjust Optional boolean value on whether to perform adjustments of
#' values prior to scoring. Default = FALSE but may be TRUE for certain
#' metrics.
#' @param cols2keep Column names of fun.DF to retain in the output. Uses
#' column names.
#' @param MetricSort How metric names should be sort; NA = as is
#' , AZ = alphabetical. Default = NULL.
#' @param boo.Shiny Boolean value for if the function is accessed via Shiny.
#' Default = FALSE.
#' @param verbose Include messages to track progress. Default = FALSE
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @export
metric.values.coral <- function(myDF
, MetricNames = NULL
, boo.Adjust = FALSE
, cols2keep = NULL
, MetricSort = NA
, boo.Shiny = FALSE
, verbose) {
# define pipe
`%>%` <- dplyr::`%>%`
time_start <- Sys.time()
# not carrying over from previous
names(myDF) <- toupper(names(myDF))
debug_sub_community <- "CORAL"
boo_debug_bugs <- FALSE
debug_sub_num <- 0
debug_sub_num_total <- 18
# global variable bindings ----
INDEX_NAME <- INDEX_CLASS <- SAMPLEID <- TAXAID <- BCG_ATTR <- WEEDY <- PHYLUM <-
CLASS <- SUBCLASS <- ORDER <- FAMILY <- GENUS <- SUBGENUS <- SPECIES <- JUVENILE <-
LRBC <- TOTTRANLNGTH_M <- DIAMMAX_CM <- DIAMPERP_CM <- HEIGHT_CM <- MORPHCONVFACT <-
TOTMORT_PCT <- WEEDY_CONFIRMED <- DIAM_CM <- R2 <- CSA <- LIVETISSUE_PCT <-
LCSA <- LCSA3D_samp_m2 <- LCSA3D_BCG_att1234_m2 <- LCSA3D_LRBC_m2 <-
ncol_AcroOrbi_m2 <- nt_BCG_att123 <- nt_BCG_att1234 <- nt_total <- pcol_Acropora <-
pcol_SmallWeedy <- pt_BCG_att5 <- ncol_Acropora <- ncol_SmallWeedy <-
nt_BCG_att5 <- NULL
# QC----
## QC, Missing Cols ----
if (verbose == TRUE) {
debug_topic <- "QC, missing cols"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
# QC, Required Fields
col.req_character <- c("SAMPLEID", "TAXAID", "BCG_ATTR", "WEEDY", "PHYLUM"
, "CLASS", "SUBCLASS", "ORDER", "FAMILY"
, "GENUS", "SUBGENUS", "SPECIES")
col.req_logical <- c("JUVENILE", "LRBC")
col.req_numeric <- c("TOTTRANLNGTH_M", "DIAMMAX_CM", "DIAMPERP_CM"
, "HEIGHT_CM", "MORPHCONVFACT", "TOTMORT_PCT")
col.req <- c(col.req_character, col.req_logical, col.req_numeric)
col.req.missing <- col.req[!(col.req %in% toupper(names(myDF)))]
col.req.missing_char <- col.req_character[!(col.req_character %in% toupper(names(myDF)))]
col.req.missing_log <- col.req_logical[!(col.req_logical %in% toupper(names(myDF)))]
col.req.missing_num <- col.req_numeric[!(col.req_numeric %in% toupper(names(myDF)))]
num.col.req.missing <- length(col.req.missing)
num.col.req.missing_char <- length(col.req.missing_char)
num.col.req.missing_log <- length(col.req.missing_log)
num.col.req.missing_num <- length(col.req.missing_num)
# Trigger prompt if any missing fields (and session is interactive)
if (num.col.req.missing != 0) {
# Create prompt for missing columns
myPrompt.01 <- paste0("There are ",num.col.req.missing," missing fields in the data:")
myPrompt.02 <- paste(col.req.missing, collapse = ", ")
myPrompt.03 <- "If you continue the metrics associated with these fields will be invalid."
myPrompt.04 <- "For example, if the BCG_ATTR field is missing all BCG-related metrics will not be correct."
myPrompt.05 <- "Do you wish to continue (YES or NO)?"
myPrompt <- paste(" "
, myPrompt.01
, myPrompt.02
, " "
, myPrompt.03
, myPrompt.04
, myPrompt.05
, sep = "\n")
user.input <- NA
if (interactive() == TRUE & boo.Shiny == FALSE) {
#user.input <- readline(prompt=myPrompt)
user.input <- utils::menu(c("YES", "NO"), title = myPrompt)
} else {
message(myPrompt)
message("boo.Shiny == TRUE and interactive == FALSE
so prompt skipped and value set to '1'.")
user.input <- 1
}## IF ~ interactive & boo.Shiny
# any answer other than "YES" will stop the function.
if (user.input != 1) {
stop(paste("The user chose *not* to continue due to missing fields: "
, paste(paste0(" ",col.req.missing), collapse = "\n"), sep = "\n"))
}##IF.user.input.END
# Add missing fields
#myDF[, col.req.missing] <- NA
if (num.col.req.missing_char > 0) {
myDF[, col.req.missing_char] <- NA_character_
}
if (num.col.req.missing_log > 0) {
myDF[, col.req.missing_log] <- NA
}
if (num.col.req.missing_num > 0) {
myDF[, col.req.missing_num] <- NA_real_
}
warning(paste("Metrics related to the following fields are invalid:"
, paste(paste0(" ", col.req.missing)
, collapse = "\n")
, sep = "\n"))
}##IF.num.col.req.missing.END
# message col names
if (verbose == TRUE) {
debug_topic <- "colnames"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
msg <- paste(msg
, paste(" ", names(myDF), collapse = "\n")
, sep = "\n")
message(msg)
}## IF ~ verbose
## QC, Cols2Keep ----
# remove duplicates with required so no errors, e.g., SAMPLEID
cols2keep <- cols2keep[!cols2keep %in% col.req]
## QC, LRBC----
# ensure TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, LRBC"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "LRBC"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
LRBC.T <- sum(myDF$LRBC == TRUE, na.rm = TRUE)
if (LRBC.T == 0) {
warning("LRBC column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.LRBC.T.END
## QC, Juvenile----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Juvenile"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "JUVENILE"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
JUVENILE.T <- sum(myDF$JUVENILE == TRUE, na.rm = TRUE)
if (JUVENILE.T == 0) {
warning("JUVENILE column does not have any TRUE values. \n Valid values are TRUE or FALSE. \n Other values are not recognized.")
}##IF.JUVENILE.T.END
## QC, Weedy----
# ensure as TRUE/FALSE
if (verbose == TRUE) {
debug_topic <- "QC, cols, values, Weedy"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "WEEDY"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
weedy_values <- c("Never", "Sometimes")
# Extract the "Weedy" column
weedy_column <- unique(myDF[, "WEEDY"])
# Check if there are any values not in the acceptable list
if (any(!weedy_column %in% weedy_values)) {
warning("WEEDY column contains unrecognized values. \n Valid values are 'Never', 'Sometimes', or'Always'. \n Other values are not recognized.")
}##IF.WEEDY.END
## QC, Mortality ----
if (any(myDF$TOTMORT_PCT > 100)) {
warning("TOTMORT_PCT column contains values outside the normal range of 0-100. \n Fix invalid values before proceeding because LCSA-based metrics will not be calculated correctly.")
}##IF.Mort.END
## QC, BCG_Attr ----
# need as character, if complex all values fail
if (verbose == TRUE) {
debug_topic <- "QC, cols, complex, BCG_Attr"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
myCol <- "BCG_ATTR"
col_TF <- myCol %in% names(myDF)
msg <- paste0("Column (", myCol, ") exists; ", col_TF)
message(msg)
}## IF ~ verbose
BCG_Complex <- is.complex(myDF[, "BCG_ATTR"])
# only tigger if have a complex field
if (BCG_Complex == TRUE) {
if (interactive() & boo.Shiny == FALSE) {
msg <- "**BCG_ATTR is complex!**"
msg2 <- "BCG metrics will not calculate properly."
msg3 <- "Reimport data with column class defined."
msg4 <- "Use either Fix1 or Fix2. Replace 'foo.csv' with your file."
msg5 <- ""
msg6 <- "# Fix 1, base R"
msg7 <- "df_data <- read.csv('foo.csv', colClass=c('BCG_Attr'='character'))"
msg8 <- ""
msg9 <- "# Fix 2, tidyverse"
msg10 <- "# install package if needed and load it"
msg11 <- "if(!require(readr)) {install.packages('readr')}"
msg12 <- "# import file and convert from tibble to data frame"
msg13 <- "df_data <- as.data.frame(read_csv('foo.csv'))"
msg14 <- ""
#
message(paste(msg, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9, msg10
, msg11, msg12, msg13, msg14, sep = "\n"))
}## IF ~ interactive & boo.Shiny == FALSE
if (interactive() == FALSE | boo.Shiny == TRUE) {
# > df$BCG_Attr_char <- as.character(df$BCG_Attr)
# > df$BCG_Attr_char <- sub("^0\\+", "", df$BCG_Attr_char)
# > df$BCG_Attr_char <- sub("\\+0i$", "", df$BCG_Attr_char)
# > table(df$BCG_Attr, df$BCG_Attr_char)
myDF[, "BCG_ATTR"] <- as.character(myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("^0\\+", "", myDF[, "BCG_ATTR"])
myDF[, "BCG_ATTR"] <- sub("\\+0i$", "", myDF[, "BCG_ATTR"])
}## IF ~ interactive() == FALSE | boo.Shiny == TRUE
}##IF ~ BCG_Attr ~ END
# Data Munging----
# Convert columns to upper case
if (verbose == TRUE) {
debug_topic <- "Munging, text cols, toupper"
debug_sub_num <- debug_sub_num + 1
msg <- paste0("debug_metval_sub, "
, debug_sub_community
, ", "
, debug_sub_num
, "/"
, debug_sub_num_total
, ", "
, debug_topic)
message(msg)
}## IF ~ verbose
col2upper <- col.req_character[!(col.req_character %in%
c("SAMPLEID", "INDEX_NAME", "INDEX_CLASS"))]
for (i in col2upper) {
myDF[, i] <- toupper(myDF[, i])
}## FOR ~ i ~ END
# Do some calcs
myDF <- myDF %>%
dplyr::mutate(WEEDY_CONFIRMED = dplyr::case_when((WEEDY == "NEVER") ~ FALSE
, (WEEDY == "SOMETIMES"
& TAXAID != "SIDERASTREA SIDEREA"
& TAXAID != "STEPHANOCOENIA INTERSEPTA"
& DIAMMAX_CM < 75) ~ TRUE
, ((TAXAID == "SIDERASTREA SIDEREA"
| TAXAID == "STEPHANOCOENIA INTERSEPTA")
& DIAMMAX_CM <= 30
& HEIGHT_CM <= 10) ~ TRUE
, ((TAXAID == "SIDERASTREA SIDEREA"
| TAXAID == "STEPHANOCOENIA INTERSEPTA")
& DIAMMAX_CM > 30
& HEIGHT_CM > 10) ~ FALSE
, TRUE ~ FALSE)
, DIAM_CM = dplyr::case_when((!is.na(DIAMPERP_CM)
& !is.na(DIAMMAX_CM))
~ as.numeric((DIAMPERP_CM + DIAMMAX_CM)/2)
, TRUE ~ as.numeric(DIAMMAX_CM))
, R2 = ((HEIGHT_CM + (DIAM_CM/2))/2)^2
, CSA = R2*MORPHCONVFACT*pi
, LIVETISSUE_PCT = 100 - TOTMORT_PCT
, LCSA = CSA * (LIVETISSUE_PCT/100)) %>%
dplyr::select(-c(R2, LIVETISSUE_PCT))
# Metric Calc----
# Calculate Metrics (could have used pipe, %>%)
met.val <- dplyr::summarise(dplyr::group_by(myDF
, SAMPLEID
, INDEX_NAME
, INDEX_CLASS)
# Transect width 1m
, transect_area_m2 = max(TOTTRANLNGTH_M, na.rm = TRUE) * 1
## Individuals ----
, ncol_total = dplyr::n()
, lcol_total = log(ncol_total)
## Number of Taxa ----
, nt_total = dplyr::n_distinct(TAXAID, na.rm = TRUE)
## Percent of Taxa ----
## Number of Individuals ----
, ncol_Acropora = sum(GENUS == "ACROPORA", na.rm = TRUE)
, ncol_AcroOrbi_m2 = sum((GENUS == "ACROPORA" | GENUS == "ORBICELLA")
, na.rm = TRUE) / transect_area_m2
## Percent of Individuals ----
, pcol_Acropora = 100 * ncol_Acropora / ncol_total
## BCG ----
### BCG, nt ####
, nt_BCG_att123 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3")]
, na.rm = TRUE)
, nt_BCG_att1234 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE)
, nt_BCG_att5 = dplyr::n_distinct(TAXAID[(BCG_ATTR == "5")]
, na.rm = TRUE)
### BCG, pt ####
, pt_BCG_att5 = 100 * nt_BCG_att5 / nt_total
## Surface Area ----
, LCSA3D_samp_m2 = sum(LCSA, na.rm = TRUE) / transect_area_m2
, LCSA3D_BCG_att1234_m2 = sum(LCSA[(BCG_ATTR == "1"
| BCG_ATTR == "2"
| BCG_ATTR == "3"
| BCG_ATTR == "4")]
, na.rm = TRUE) / transect_area_m2
, LCSA3D_LRBC_m2 = sum(LCSA[(LRBC == TRUE)]
, na.rm = TRUE) / transect_area_m2
## Weedy ----
### Weedy, ncol ####
, ncol_SmallWeedy = sum(WEEDY_CONFIRMED == TRUE, na.rm = TRUE)
### Weedy, pcol ####
, pcol_SmallWeedy = 100 * ncol_SmallWeedy / ncol_total
)##met.val.END
}##FUNCTION.metric.values.coral.END
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