Format p-values for Rmarkdown publications

format_pval.R

#################################################
## Format p-values for use in Rmarkdown documents
## This function modifies base::format.pval() to automate
## the inclusion of equalities and inequalities
## Author: W.K. Petry
#################################################
# Arguments:
# pv            a numeric vector
# digits        how many significant digits to use; recommended value is 3
# eps           numerical tolerance; effectively the smallest p-value to report; recommended value is 10^(-digits)
# na.form       character representation of NAs in the output
# appendequal   logical; whether or not to add a leading "=" when 10^(-digits) < pv < 1-10^(-digits)
# sep           character separator between the (in)equality symbol and the formatted p-value

# Value:
# A character vector.

# Examples:
# my_pvals <- c(stats::runif(5), pi^-100, NA)
# base::format.pval(my_pvals)
# format_pval(my_pvals)
# 
# more_pvals <- c(0.1, 0.0001, 1e-27)
# format_pval(more_pvals)
# format_pval(more_pvals, digits = 3, eps = 10^-3)
# format_pval(more_pvals, digits = 3, eps = 10^-6)
# 
# format_pval(more_pvals, appendequal = FALSE, sep = "")
#################################################

format_pval <- function (pv, digits = max(1L, getOption("digits") - 2L),
                         eps = .Machine$double.eps, na.form = "NA",
                         appendequal = TRUE, sep = " ", ...) {
  if ((has.na <- any(ina <- is.na(pv)))) 
    pv <- pv[!ina]
  r <- character(length(is0 <- pv < eps))
  is1 <- (1 - pv) < 10^-digits
  if (any(!is0 & !is1)) {
    rr <- pv <- pv[!is0 & !is1]
    expo <- floor(log10(ifelse(pv > 0, pv, 1e-50)))
    fixp <- expo >= -3 | (expo == -4 & digits > 1)
    if (any(fixp)) 
      rr[fixp] <- format(pv[fixp], digits = digits, ...)
    if (any(!fixp)) 
      rr[!fixp] <- format(pv[!fixp], digits = digits, ...)
    r[!is0 & !is1] <- if (appendequal == TRUE) 
      paste("=", rr)
    else rr
  }
  if (any(is0)) {
    r[is0] <- paste("<", format(eps, digits = digits, ...), 
                    sep = sep)
  }
  if (any(is1)) {
    r[is1] <- paste(">", format(1-10^-digits, digits = digits, ...), 
                    sep = sep)
  }
  if (has.na) {
    rok <- r
    r <- character(length(ina))
    r[!ina] <- rok
    r[ina] <- na.form
  }
  r
}