R/sample.r

In SCCWRP/BMIMetrics: Suite of metric calculators for benthic macroinvertebrate communities

#' Sample Bug Results
#' 
#' Takes bug data and subsamples those that have more than 500 individuals in the sample
#' 
#' @param x An object of class BMIagg
#' @S3method sample BMI
#' @S3method sample default
#' @export 
#' @import vegan
#' @include loadMetaData.r 


sample <- function(x, ...){
  UseMethod("sample", x)
}

sample.default <- function (x, size, replace = FALSE, prob = NULL) 
{
  if (length(x) == 1L && is.numeric(x) && x >= 1) {
    if (missing(size)) 
      size <- x
    .Internal(sample(x, size, replace, prob))
  }
  else {
    if (missing(size)) 
      size <- length(x)
    x[.Internal(sample(length(x), size, replace, prob))]
  }
}

sample.BMI <- function(x, number=500){
  x$SampleID <- as.character(x$SampleID)
  x$originalBAResult <- x$BAResult
  #   rarifydown <- function(data){
  #     unlist(sapply(unique(data$SampleID), function(sample){
  #       v <- data[data$SampleID==sample, "BAResult"]
  #       if(sum(v)>=number){rrarefy(v, number)} else
  #       {v}
  #     }))}
  #   x$BAResult <- rarifydown(x) 
  
  x <- ddply(x, .(SampleID), function(data){
    if(sum(data$BAResult)>=number)
      data$BAResult <- as.vector(rrarefy(data$BAResult, number))
    data
  })
  x <- subset(x, BAResult != 0)
  x$SampleID <- as.factor(x$SampleID)
  class(x) <- c("BMIsub", "BMI", "data.frame")
  x
}