R/trim.var.R

In DistanceDevelopment/dsm: Density Surface Modelling of Distance Sampling Data

#' Trimmed variance
#'
#' Trim the variance estimates from the bootstrap. This is defined as the
#' percentage defined as amount necessary to bring median and trimmed mean
#' within 8% of each other these are defined as 'outliers'.
#'
#' @param untrimmed.bootstraps (usually the `$study.area.total` element of a
#' returned [`dsm.var.movblk`][dsm.var.movblk] bootstrap object.
#' @param boxplot.coef the value of `coef` used to calculate the outliers see
#' [`boxplot`][graphics::boxplot].
#'
#' @return trimmed variance
#'
#' @export
#' @importFrom stats var
#' @importFrom grDevices boxplot.stats
#' @author Louise Burt
trim.var <- function(untrimmed.bootstraps, boxplot.coef=1.5){
  outliers <- boxplot.stats(untrimmed.bootstraps, coef=boxplot.coef)$out
  bootstrap.abund <-untrimmed.bootstraps[!(untrimmed.bootstraps %in% outliers)]

  ret <- var(bootstrap.abund)

  attr(ret,"trim.prop") <- length(outliers) / length(untrimmed.bootstraps)
  attr(ret,"untrimn") <- length(untrimmed.bootstraps)
  attr(ret,"outliers") <- length(outliers)
  attr(ret,"trim.ind") <- !(untrimmed.bootstraps %in% outliers)
  attr(ret,"boxplot.coef") <- boxplot.coef

  return(ret)
}