In leppott/BCGcalc: Biological Condition Gradient, calculator

knitr::opts_chunk$set(echo = FALSE
                      , results = 'asis'
                      , warning = FALSE
                      , message = FALSE)

Required Fields

The following fields are required in input files.

Click here to download an Excel file with this table plus example data.

# Packages
library(readxl)
#library(DT)

# Data
fn_req <- "BCGcalc_ReqFields_20230203.xlsx"
path_req <- file.path("files", fn_req)
df_req <- read_excel(path_req, sheet = "RequiredFields")

# Table (DT)
cap_req <- "Table 1. Required fields."
# DT::datatable(df_req
#               , filter = "top"
#               , caption = cap_req
#               , options = list(scrollX = TRUE
#                                , autoWidth = TRUE)
#               )
# DT::datatable(iris) # not working correctly in fragment
knitr::kable(df_req, caption = cap_req)

Optional Fields

Fields necessary to calculate other metrics can be included and do not affect the BCG model output. Additional metrics are available in the '*metval_all.csv' file.

# Packages
#library(DT)

# Table
col1 <- rep("Optional", 5)
col2 <- c("THERMAL_INDICATOR"
          , "TOLVAL"
          , "HABIT"
          , "NOTEWORTHY"
          , "LONGLIVED") 
col3 <- c("text", "numeric", rep("text", 3))
col4 <- c("stenoc, cold, cool, cowa, warm, stenow, eurythermal"
          , "number ranging from 0-10"
          , "BU, CB, CN, SP, SW"
          , "TRUE, FALSE"
          , "TRUE, FALSE")
d1 <- "Thermal preference assignment based on Stamp et al. (in progress): stenoc=cold stenotherm; cold, cool, cowa = cool/warm, warm, stenow = warm stenotherm, eurythermal."
d2 <- "Taxa with tolerance values ranging from 0 to 3 are considered 'intolerant' to anthropogenic disturbance and are included in the 'intolerant' metric calculations. Those with values ranging from 7 to 10 are included in the 'tolerant' metrics."
d3 <- "Habit. Multiple entries are allowed and should be separated with a comma. Entries: burrowers (BU), climbers (CB), clingers (CN), sprawlers (SP), swimmers (SW)."
d4 <- "Noteworthy taxa occur most often at sites with complex and resilient habitat structure that supports high overall freshwater biodiversity. Most of these taxa are rarely or occasionally encountered in benthic macroinvertebrate biomonitoring samples."
d5 <- "These invertebrates require more than one year to complete their life cycles; thus, they are exposed to all the human activities that influence the stream throughout one or more years. If the stream is dry part of the year or subject to flooding, these animals may disappear. Loss of long-lived taxa may also indicate an on-going problem that repeatedly interrupts their life cycles"
col5 <- c(d1, d2, d3, d4, d5)

df_opt <- data.frame(cbind(col1, col2, col3, col4, col5))
names(df_opt) <- c("Column Type"
                   , "Column Name"
                   , "Data Type"
                   , "Allowable Entries"
                   , "Comment")
cap_opt <- "Table 2. Optional fields"
# DT::datatable(df_opt
#               , filter = "top"
#               , caption = cap_opt
#               , options = list(scrollX = TRUE
#                                , autoWidth = TRUE)
#               )
knitr::kable(df_opt, caption = cap_opt)