#' @name Climber
#' @title Climber
#'
#' Calculates metrics related to the climber habit group.
#'
#' @param x An object of class BMIprc or BMIagg
#'
#' @usage
#' Climber_Percent(x)
#' Climber_PercentTaxa(x)
#' Climber_Taxa(x)
#'
#' @export Climber_Percent
#' @export Climber_PercentTaxa
#' @export Climber_Taxa
#' @S3method Climber_Percent BMIagg
#' @S3method Climber_PercentTaxa BMIagg
#' @S3method Climber_Taxa BMIagg
#' @S3method Climber_Percent BMIprc
#' @S3method Climber_PercentTaxa BMIprc
#' @S3method Climber_Taxa BMIprc
#' @import plyr
#' @include loadMetaData.r
Climber_Percent <- function(x){
UseMethod("Climber_Percent", x)
}
Climber_PercentTaxa <- function(x){
UseMethod("Climber_PercentTaxa", x)
}
Climber_Taxa <- function(x){
UseMethod("Climber_Taxa", x)
}
Climber_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Habit == "CB")])/sum(df$BAResult.subsample)
})
}
Climber_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Habit == "CB")])/sum(df$BAResult)
})
}
Climber_PercentTaxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x[x$BAResult.subsample >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(df[!duplicated(df$SAFIT1) & df$Habit == "CB", ])/nrow(df[!duplicated(df[, "SAFIT1"]),])
})
}
Climber_PercentTaxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x[x$BAResult >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(df[!duplicated(df$SAFIT1) & df$Habit == "CB", ])/nrow(df[!duplicated(df[, "SAFIT1"]),])
})
}
Climber_Taxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x[x$BAResult.subsample >0 & x$distinct_SAFIT1 == "Distinct",], "SampleID", function(df){
nrow(df[!duplicated(df$SAFIT1) & df$Habit == "CB", ])
})
}
Climber_Taxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Habit")])
ddply(x[x$BAResult >0 & x$distinct_SAFIT1 == "Distinct", ], "SampleID", function(df){
nrow(df[!duplicated(df$SAFIT1) & df$Habit == "CB", ])
})
}
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