R/pvalueFormatter.R

In raredd/Gmisc0: Collection of functions for plotting relations, generating tables, and more.

#' Formats the p-values
#'
#' Gets formatted p-values. For instance
#' you often want 0.1234 to be 0.12 while also
#' having two values up until a limit,
#' i.e. 0.01234 should be 0.012 while
#' 0.001234 should be 0.001. Furthermore you
#' want to have < 0.001 as it becomes ridiculous
#' to report anything below that value.
#'
#' @param pvalues The p-values
#' @param two_dec.limit The limit for showing two decimals
#' @param sig.limit The significance limit for < sign
#' @param html If the less than sign should be < or &lt;
#'  as needed for html output.
#' @return vector
#'
#' @examples pvalueFormatter(c(0.10234,0.010234, 0.0010234, 0.000010234))
#' @export
pvalueFormatter <- function(pvalues, two_dec.limit = 10^-2,
    sig.limit = 10^-4, html=TRUE){
  if (is.logical(html))
    html <- ifelse(html, "&lt; ", "< ")
  sapply(pvalues, function(x, two_dec.limit, sig.limit, lt_sign){
      if (is.na(as.numeric(x))){
        warning("The value: '", x, "' is non-numeric and pvalueFormatter",
                " can't therfore handle it")
        return (x)
      }

      if (x < sig.limit)
        return(sprintf("%s%s", lt_sign, format(sig.limit, scientific=FALSE)))

      if (x > two_dec.limit)
        return(format(x,
                      digits=2,
                      nsmall=-floor(log10(x))+1))

      return(format(x, digits=1, scientific=FALSE))
    }, sig.limit=sig.limit,
    two_dec.limit = two_dec.limit,
    lt_sign = html)
}