In leppott/MMIcalc: Calculate multi-metric index (MMI) values and scores.

This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.

Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter.

##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Library Name
myLibrary <- "MMIcalc" # "ContDataQC","MMIcalc","MMIcalcNV","MBSStools","XC95"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# files to library folder
# file.copy("metric.values.R","./Library/MMIcalc/R/metric.values.R",overwrite=TRUE)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
myLibrary <- "MMIcalc"
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Restart R within RStudio:  Ctrl + Shift + F10
library(MMIcalc)
?metric.values

Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Ctrl+Alt+I.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Ctrl+Shift+K to preview the HTML file).

Testing Metric Value Code

# Bugs
myDF        <- myDF.Bugs
SampleID    <- "SampleID"
MetricNames <- myMetrics.Bugs

# Fish
myDF        <- myDF.Fish
SampleID    <- "SampleID"
MetricNames <- myMetrics.Fish

save bug data for QC

write.csv(myMetric.Values.Bugs,"bibi_genus.csv")

QC

myDF.Bugs <- taxa_bugs_genus
x <- myDF.Bugs
y <- subset(myDF.Bugs, StationID=="PATL-B05-X-2016")

Metric Adjustment

Reference table

Method = Observed / Expected

Calculation of Expected (E) Linear is y = m*x +b

MBSS has 1 metric, nt_benthic, that is in 3 of the 4 strata that needs adjustment.

myMetric.Values.Fish[,"nt_benthic_Obs"] <- myMetric.Values.Fish[,"nt_benthic"]
# Expected constants
## m
myMetric.Values.Fish[,"nt_benthic_m"] <- NA
myMetric.Values.Fish[,"nt_benthic_m"][myMetric.Values.Fish[,"Index.Region"]=="COASTAL"]   <- 1.69
myMetric.Values.Fish[,"nt_benthic_m"][myMetric.Values.Fish[,"Index.Region"]=="EPIEDMONT"] <- 1.25
myMetric.Values.Fish[,"nt_benthic_m"][myMetric.Values.Fish[,"Index.Region"]=="HIGHLAND"]  <- 1.23
## b
myMetric.Values.Fish[,"nt_benthic_b"] <- NA
myMetric.Values.Fish[,"nt_benthic_b"][myMetric.Values.Fish[,"Index.Region"]=="COASTAL"]   <- -3.33
myMetric.Values.Fish[,"nt_benthic_b"][myMetric.Values.Fish[,"Index.Region"]=="EPIEDMONT"] <- -2.36
myMetric.Values.Fish[,"nt_benthic_b"][myMetric.Values.Fish[,"Index.Region"]=="HIGHLAND"] <- -2.35
# Calc Expected
myMetric.Values.Fish[,"nt_benthic_Exp"] <- (myMetric.Values.Fish[,"nt_benthic_m"] * log10(myMetric.Values.Fish[,"Catchment"])) + myMetric.Values.Fish[,"nt_benthic_b"]
# Calc Adjusted
myMetric.Values.Fish[,"nt_benthic_Adj"] <- myMetric.Values.Fish[,"nt_benthic_Obs"] / myMetric.Values.Fish[,"nt_benthic_Exp"]
# Rename base metric with adjusted value
myMetric.Values.Fish[,"nt_benthic"] <- myMetric.Values.Fish[,"nt_benthic_Adj"]