R/spm_P_Bonf.R

In jpellman/spmR: Statistical Parametric Mapping in R

#' @name spm_P_Bonf
#function P = spm_P_Bonf(Z,df,STAT,S,n)
#' @title SPM: Returns the corrected P value using Bonferroni
#' @usage P = spm_P_Bonf(Z,df,STAT,S,n)
#
#' @param Z     - height {minium over n values}
#' @param df    - [df{interest} df{error}]
#' @param STAT  - Statistical field
#'       'Z' - Gaussian field
#'       'T' - T - field
#'       'X' - Chi squared field
#'       'F' - F - field
#' @param n     - number of conjoint SPMs
#' @param S     - Voxel count
#
#' @return P     - corrected   P value  - P(STAT > Z)
#
#___________________________________________________________________________
#
#' @description spm_P_Bonf returns the p-value of Z corrected by the Bonferroni
#' inequality. 
#'
#' If n > 1 a conjunction probility over the n values of the statistic
#' is returned
#
#___________________________________________________________________________
# MATLAB version: Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging

spm_P_Bonf <- function(Z,df,STAT,S,n) {

   if(STAT == "Z") {
        P <- 1 - pnorm(Z)
    } else if(STAT == "T") {
        P <- 1 - pt(Z, df[2])
    } else if(STAT == "X") {
        P <- 1 - pchisq(Z, df[2])
    } else if(STAT == "F") {
        P <- 1- pf(Z, df[1], df[2])
    } else {
        stop("wrong value for STAT argument", STAT)
    }

    P <- S*P^n
    P <- min(P, 1.0)

    P
}