R/pIntrinsic.R

In ReplicationSuccess: Design and Analysis of Replication Studies

#' Computes the p-value for intrinsic credibility
#'
#' @param p numeric vector of p-values.
#' @param z numeric vector of z-values. Default is \code{NULL}.
#' @param alternative  Either "two.sided" (default) or "one.sided".
#' Specifies if the p-value is two-sided or one-sided.
#' If the p-value is one-sided, then a one-sided p-value for
#' intrinsic credibility is computed.
#' @param type   Type of intrinsic p-value. Default is "Held" as in
#' Held (2019). The other option is "Matthews" as in Matthews (2018).
#' @return p-values for intrinsic credibility.
#'
#' @references Matthews, R. A. J. (2018). Beyond 'significance': principles and
#'     practice of the analysis of credibility. \emph{Royal Society Open
#'     Science}, \bold{5}, 171047. \doi{10.1098/rsos.171047}
#'
#' Held, L. (2019). The assessment of intrinsic credibility and a new argument
#' for \emph{p < 0.005}. \emph{Royal Society Open Science}, \bold{6}, 181534.
#' \doi{10.1098/rsos.181534}
#' @author Leonhard Held
#' @examples
#' p <- c(0.005, 0.01, 0.05)
#' pIntrinsic(p = p)
#' pIntrinsic(p = p, type = "Matthews")
#' pIntrinsic(p = p, alternative = "one.sided")
#' pIntrinsic(p = p, alternative = "one.sided", type = "Matthews")
#'
#' pIntrinsic(z = 2)
#' @export
pIntrinsic <- function(p = z2p(z, alternative = alternative), z = NULL,
                       alternative = c("two.sided", "one.sided", "less", "greater"),
                       type = c("Held", "Matthews")){
    stopifnot(is.numeric(p),
              length(p) > 0,
              is.finite(p),
              0 < p, p <= 1,
              
              is.null(z) || (is.numeric(p) && length(p) > 0 && all(is.finite(p))),
              
              !is.null(alternative))
    alternative <- match.arg(alternative)
    
    stopifnot(!is.null(type))
    type <- match.arg(type)
    
    if(type == "Held"){
        iz <- p2z(p, alternative = alternative)/sqrt(2)
        iP <- z2p(z = iz, alternative = alternative)
    } else{ ## type == "Matthews"
        iz <- p2z(p, alternative = alternative)/sqrt(2)*sqrt(sqrt(5) - 1)
        iP <- z2p(z = iz, alternative = alternative)
    }
    return(iP)
}