#' @name Predator
#' @title Predator related metrics
#'
#' @param x An object of class BMIprc or BMIagg
#'
#' @usage
#' Predator_Percent(x)
#' Predator_PercentTaxa(x)
#' Predator_Taxa(x)
#'
#' @export Predator_Percent
#' @export Predator_PercentTaxa
#' @export Predator_Taxa
#' @S3method Predator_Percent BMIagg
#' @S3method Predator_PercentTaxa BMIagg
#' @S3method Predator_Taxa BMIagg
#' @S3method Predator_Percent BMIprc
#' @S3method Predator_PercentTaxa BMIprc
#' @S3method Predator_Taxa BMIprc
#' @import plyr
#' @include loadMetaData.r
Predator_Percent <- function(x){
UseMethod("Predator_Percent", x)
}
Predator_PercentTaxa <- function(x){
UseMethod("Predator_PercentTaxa", x)
}
Predator_Taxa <- function(x){
UseMethod("Predator_Taxa", x)
}
Predator_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$FunctionalFeedingGroup == "P")])/sum(df$BAResult.subsample)
})
}
Predator_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$FunctionalFeedingGroup == "P")])/sum(df$BAResult)
})
}
Predator_PercentTaxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x[x$BAResult.subsample >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(unique(df[which(df$FunctionalFeedingGroup == "P"), ]))/nrow(df[!duplicated(df[, "SAFIT1"]),])
})
}
Predator_PercentTaxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x[x$BAResult >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(unique(df[which(df$FunctionalFeedingGroup == "P"), ]))/nrow(df[!duplicated(df[, "SAFIT1"]),])
})
}
Predator_Taxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x[x$BAResult.subsample >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(unique(df[which(df$FunctionalFeedingGroup == "P"), ]))
})
}
Predator_Taxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "FunctionalFeedingGroup")])
ddply(x[x$BAResult >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(df[which(df$FunctionalFeedingGroup == "P"), ])
})
}
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