#' @title Compute BMI metrics for CSCI
#'
#' Computes all CSCI related BMI metrics. This includes, clinger percent taxa, coleoptera,
#' percent taxa, taxnomic richness, EPT percent taxa, number of shredder taxa, and percent
#' of individuals that are intolerant.
#'
#' @param x An object of class BMIagg or BMIprc
#' @export BMICSCI
#' @import dplyr
#' @import vegan
#' @import plyr
BMICSCI <- function(x, effort=2){
stopifnot("BMIagg" %in% class(x))
x <- x[[effort]]
x$Habit <- as.character(x$Habit)
x <- plyr::rename(x, c("distinct_SAFIT1" = "distinct_SAFIT2", "SAFIT2" = "iggSAFIT2", "SAFIT1" = "SAFIT2"),
warn_missing=FALSE)
out <- dplyr::summarise(dplyr::group_by(x, SampleID),
Taxonomic_Richness = sum1(distinct_SAFIT2=="Distinct"),
Intolerant_Percent = sum1(BAResult[which(ToleranceValue <= 2)])/sum1(BAResult[!is.na(ToleranceValue)]),
Shredder_Taxa = sum1(distinct_SAFIT2=="Distinct" & (FunctionalFeedingGroup == "SH")),
Clinger_PercentTaxa = sum1(distinct_SAFIT2=="Distinct" & Habit == "CN")/sum1(distinct_SAFIT2=="Distinct" & !is.na(Habit)),
Coleoptera_PercentTaxa = sum1(distinct_SAFIT2=="Distinct" & (Order == "Coleoptera"))/sum1(distinct_SAFIT2=="Distinct"),
EPT_PercentTaxa = sum1(distinct_SAFIT2=="Distinct" & (Order %in% c("Ephemeroptera", "Plecoptera", "Trichoptera")))/sum1(distinct_SAFIT2=="Distinct")
)
# change na values in Clinger_PercentTaxa, Intolerant_Percent to zero
out$Intolerant_Percent[is.na(out$Intolerant_Percent)] <- 0
out$Clinger_PercentTaxa[is.na(out$Clinger_PercentTaxa)] <- 0
return(out)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.