#' @name Chironomidae
#' @title Chironomidae related metrics
#'
#' @description Calculates metrics related to chironomids.
#'
#' @usage
#' Chironomidae_PercentTaxa(x)
#' Chironomidae_Taxa(x)
#' Chironominae_Percent(x)
#' Chironominae_PercentOfMidges(x)
#' Tanypodinae_Percent(x)
#' Tanypodinae_PercentOfMidges(x)
#'
#' @param x An object of class BMIprc or BMIagg
#' @export Chironomidae_PercentTaxa
#' @export Chironomidae_Taxa
#' @export Chironominae_Percent
#' @export Chironominae_PercentOfMidges
#' @export Tanypodinae_Percent
#' @export Tanypodinae_PercentOfMidges
#' @export Orthocladiinae_PercentOfMidges
#' @S3method Chironomidae_PercentTaxa BMIagg
#' @S3method Chironomidae_Taxa BMIagg
#' @S3method Chironominae_Percent BMIagg
#' @S3method Chironominae_PercentOfMidges BMIagg
#' @S3method Tanypodinae_Percent BMIagg
#' @S3method Tanypodinae_PercentOfMidges BMIagg
#' @S3method Chironomidae_PercentTaxa BMIprc
#' @S3method Chironomidae_Taxa BMIprc
#' @S3method Chironominae_Percent BMIprc
#' @S3method Chironominae_PercentOfMidges BMIprc
#' @S3method Tanypodinae_Percent BMIprc
#' @S3method Tanypodinae_PercentOfMidges BMIprc
#' @S3method Orthocladiinae_PercentOfMidges BMIagg
#' @S3method Orthocladiinae_PercentOfMidges BMIprc
#' @import plyr
#' @include loadMetaData.r
Chironomidae_PercentTaxa <- function(x){
UseMethod("Chironomidae_PercentTaxa", x)
}
Chironomidae_Taxa <- function(x){
UseMethod("Chironomidae_Taxa", x)
}
Chironominae_Percent <- function(x){
UseMethod("Chironominae_Percent", x)
}
Chironominae_PercentOfMidges <- function(x){
UseMethod("Chironominae_PercentOfMidges", x)
}
Tanypodinae_Percent <- function(x){
UseMethod("Tanypodinae_Percent", x)
}
Tanypodinae_PercentOfMidges <- function(x){
UseMethod("Tanypodinae_PercentOfMidges", x)
}
Orthocladiinae_PercentOfMidges <- function(x){
UseMethod("Orthocladiinae_PercentOfMidges", x)
}
Chironomidae_PercentTaxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family")])
ddply(x[x$BAResult.subsample >0, ], "SampleID", function(df){
length(df$SAFIT2[which(df$Family == "Chironomidae")])/nrow(df)
})
}
Chironomidae_PercentTaxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family")])
ddply(x[x$BAResult >0, ], "SampleID", function(df){
length(df$SAFIT2[which(df$Family == "Chironomidae")])/nrow(df)
})
}
Chironomidae_Taxa.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family")])
ddply(x[x$BAResult.subsample >0, ], "SampleID", function(df){
length(unique(df$SAFIT2[which(df$Family == "Chironomidae")]))
})
}
Chironomidae_Taxa.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family")])
ddply(x[x$BAResult >0, ], "SampleID", function(df){
length(unique(df$SAFIT2[which(df$Family == "Chironomidae")]))
})
}
Chironominae_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Subfamily == "Chironominae")])/sum(df$BAResult.subsample)
})
}
Chironominae_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Subfamily == "Chironominae")])/sum(df$BAResult)
})
}
Tanypodinae_Percent.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Subfamily == "Tanypodinae")])/sum(df$BAResult.subsample)
})
}
Tanypodinae_Percent.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Subfamily == "Tanypodinae")])/sum(df$BAResult)
})
}
Tanypodinae_PercentOfMidges.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Subfamily == "Tanypodinae")])/sum(df$BAResult.subsample[which(df$Family == "Chironomidae")])
})
}
Tanypodinae_PercentOfMidges.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Subfamily == "Tanypodinae")])/sum(df$BAResult[which(df$Family == "Chironomidae")])
})
}
Chironominae_PercentOfMidges.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Subfamily == "Chironominae")])/sum(df$BAResult.subsample[which(df$Family == "Chironomidae")])
})
}
Chironominae_PercentOfMidges.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Subfamily == "Chironominae")])/sum(df$BAResult[which(df$Family == "Chironomidae")])
})
}
Orthocladiinae_PercentOfMidges.BMIprc <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult.subsample[which(df$Subfamily == "Orthocladiinae")])/sum(df$BAResult.subsample[which(df$Family == "Chironomidae")])
})
}
Orthocladiinae_PercentOfMidges.BMIagg <- function(x){
metadata <- loadMetaData()
x <- merge(x, metadata[, c("FinalID", "LifeStageCode", "Family", "Subfamily")])
ddply(x, "SampleID", function(df){
sum(df$BAResult[which(df$Subfamily == "Orthocladiinae")])/sum(df$BAResult[which(df$Family == "Chironomidae")])
})
}
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