#' Crustacea Related Metrics
#'
#' Calculates various metrics based on Crustacea taxa
#'
#' @param x An object of class BMIprc or BMIagg
#' @param level Either "SAFIT1" or "SAFIT2"
#' @export Crustacea_Percent
#' @export Ostracoda_Percent
#' @S3method Crustacea_Percent BMIagg
#' @S3method Crustacea_Percent BMIprc
#' @S3method Ostracoda_Percent BMIagg
#' @S3method Ostracoda_Percent BMIprc
#' @import plyr
#' @include loadMetaData.r
Crustacea_Percent <- function(x, ...){
UseMethod("Crustacea_Percent", x)
}
Ostracoda_Percent <- function(x, ...){
UseMethod("Ostracoda_Percent", x)
}
Crustacea_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x$Subphylum <- metadata$Subphylum[match(x$FinalID, metadata$FinalID)]
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[df$Subphylum =="Crustacea"])/sum(df$BAResult.subsample)
})
}
Crustacea_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x$Subphylum <- metadata$Subphylum[match(x$FinalID, metadata$FinalID)]
ddply(x, "SampleID", function(df){
sum(df$BAResult[df$Subphylum =="Crustacea"])/sum(df$BAResult)
})
}
Ostracoda_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x$Class <- metadata$Class[match(x$FinalID, metadata$FinalID)]
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[df$Class =="Ostracoda"])/sum(df$BAResult.subsample)
})
}
Ostracoda_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x$Class <- metadata$Class[match(x$FinalID, metadata$FinalID)]
ddply(x, "SampleID", function(df){
sum(df$BAResult[df$Class =="Ostracoda"])/sum(df$BAResult)
})
}
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