R/stdErrMedBoot.R

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

#' Standard Eror Of Median by Boot-Strap
#'
#' \code{stdErrMedBoot} estimate standard eror of median by bootstrap approach. 
#' Note: requires package \href{https://CRAN.R-project.org/package=boot}{boot}
#'
#' @param x (numeric) vector to estimate median and it's standard error
#' @param nBoot (integer) number for iterations
#' @param silent (logical) suppress messages
#' @param callFrom (character) allows easier tracking of messages produced
#' @param debug (logical) display additional messages for debugging
#' @return This function returns a (numeric) vector with estimated standard error
#' @seealso \code{\link{colMedSds}} and \code{\link{rowMedSds}}; based on \code{\link[boot]{boot}}
#' @examples
#' set.seed(2014); ra1 <- c(rnorm(9,2,1),runif(8,1,2))
#' rat1 <- ratioAllComb(ra1[1:9],ra1[10:17])
#' median(rat1); stdErrMedBoot(rat1)
#' @export
stdErrMedBoot <- function(x, nBoot=9, silent=FALSE, debug=FALSE, callFrom=NULL) { 
  fxNa <- .composeCallName(callFrom, newNa="stdErrMedBoot")
  if(isTRUE(debug)) silent <- FALSE else { debug <- FALSE
    if(!isTRUE(silent)) silent <- FALSE }
   
  ## uses package boot
  if(requireNamespace("boot", quietly=TRUE)) {
    median.fun <- function(dat, indices) stats::median(dat[indices], na.rm=TRUE)
    out <- try(stats::sd(boot::boot(data=x, statistic=median.fun, R=nBoot)$t))
    if(inherits(out, "try-error")) stop("Unable to run bootstrap, check format of data and argument 'nBoot'")
    out
  } else {
    if(!silent) message(fxNa,"NOTE: Package 'boot' not found ! Please install first from CRAN  (returning NULL)")
  }
}