R/RcppExports.R

In DiscreteFDR: FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests

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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' @name kernel
#' @rdname kernel
#' 
#' @title
#' Kernel Functions
#' 
#' @description
#'
#' Kernel functions that transform observed p-values or their support according
#' to \[HSU\], \[HSD\], \[AHSU\], \[AHSD\] and \[HBR-\eqn{\lambda}\]. The
#' output is used by [discrete.BH] or [DBR], respectively.
#' `kernel_DBH_crit`, `kernel_ADBH_crit` and `kernel_DBR_crit` additionally
#' compute and return the critical constants. 
#' The end user should not use these functions directly.
#' 
#' **Note**: As of version 2.0, these functions are purely internal functions!
#' As a consequence, they have to be called directly via `:::`, e.g. 
#' `DiscreteFDR:::kernel_DBH_fast()`. But users should **not** rely on them, as
#' parameters (including their names, order, etc.) may be changed without
#' notice!
#' 
#' @details
#' When computing critical constants under step-down, that is, when using
#' `kernel_DBH_crit`, `kernel_ADBH_crit` or `kernel_DBR_crit` with
#' `stepUp = FALSE` (i.e. the step-down case), we still need to get transformed
#' p-values to compute the adjusted p-values.
#' 
#' @seealso
#' [`discrete.BH`], [`fast.Discrete`], [`DBR`]
#' 
#' @templateVar pCDFlist TRUE
#' @templateVar pvalues TRUE
#' @templateVar stepUp TRUE
#' @templateVar alpha2 TRUE
#' @templateVar support TRUE
#' @templateVar sorted_pv TRUE
#' @templateVar lambda2 TRUE
#' @templateVar pCDFcounts TRUE
#' @template param 
#' 
#' @return
#' For `kernel.DBH.fast`, `kernel.ADBH.fast` and `kernel.DBR.fast`, a vector
#' of transformed p-values is returned. `kernel.DBH.crit`, `kernel.ADBH.crit`
#' `kernel.DBR.crit` return a list with critical constants (`$crit.consts`)
#' and transformed p-values (`$pval.transf`), but if `stepUp = FALSE`, there
#' are critical values only.
#' 
#' @examples \dontrun{
#' X1 <- c(4, 2, 2, 14, 6, 9, 4, 0, 1)
#' X2 <- c(0, 0, 1, 3, 2, 1, 2, 2, 2)
#' N1 <- rep(148, 9)
#' N2 <- rep(132, 9)
#' Y1 <- N1 - X1
#' Y2 <- N2 - X2
#' df <- data.frame(X1, Y1, X2, Y2)
#' df
#' 
#' # Compute p-values and their supports of Fisher's exact test
#' test.result <- generate.pvalues(df, "fisher")
#' raw.pvalues <- test.result$get_pvalues()
#' pCDFlist <- test.result$get_pvalue_supports()
#' 
#' alpha <- 0.05
#' 
#' # Compute the step functions from the supports
#' 
#' # If not searching for critical constants, we use only the observed p-values
#' sorted.pvals   <- sort(raw.pvalues)
#' y.DBH.sd.fast  <- kernel_DBH_fast(pCDFlist, sorted.pvals)
#' y.ADBH.sd.fast <- kernel_ADBH_fast(pCDFlist, sorted.pvals)
#' y.DBR.fast     <- kernel_DBR_fast(pCDFlist, sorted.pvals)
#' # transformed values
#' y.DBH.sd.fast
#' y.ADBH.sd.fast
#' y.DBR.fast
#' 
#' # compute transformed support
#' pv.list        <- sort(unique(unlist(pCDFlist)))
#' y.DBH.sd.crit  <- kernel_DBH_crit(pCDFlist, pv.list, sorted.pvals)
#' y.ADBH.sd.crit <- kernel_ADBH_crit(pCDFlist, pv.list, sorted.pvals)
#' y.DBR.crit     <- kernel_DBR_crit(pCDFlist, pv.list, sorted.pvals)
#' # critical constants
#' y.DBH.sd.crit$crit.consts
#' y.ADBH.sd.crit$crit.consts
#' y.DBR.crit$crit.consts
#' # The following exist only for step-down direction or DBR
#' y.DBH.sd.crit$pval.transf
#' y.ADBH.sd.crit$pval.transf
#' y.DBR.crit$pval.transf
#' }
#' 
NULL

#' @rdname kernel
kernel_DBH_fast <- function(pCDFlist, pvalues, stepUp = FALSE, alpha = 0.05, support = numeric(), pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_DBH_fast', PACKAGE = 'DiscreteFDR', pCDFlist, pvalues, stepUp, alpha, support, pCDFcounts)
}

#' @rdname kernel
kernel_DBH_crit <- function(pCDFlist, support, sorted_pv, stepUp = FALSE, alpha = 0.05, pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_DBH_crit', PACKAGE = 'DiscreteFDR', pCDFlist, support, sorted_pv, stepUp, alpha, pCDFcounts)
}

#' @rdname kernel
kernel_ADBH_fast <- function(pCDFlist, sorted_pv, stepUp = FALSE, alpha = 0.05, support = numeric(), pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_ADBH_fast', PACKAGE = 'DiscreteFDR', pCDFlist, sorted_pv, stepUp, alpha, support, pCDFcounts)
}

#' @rdname kernel
kernel_ADBH_crit <- function(pCDFlist, support, sorted_pv, stepUp = FALSE, alpha = 0.05, pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_ADBH_crit', PACKAGE = 'DiscreteFDR', pCDFlist, support, sorted_pv, stepUp, alpha, pCDFcounts)
}

#' @rdname kernel
kernel_DBR_fast <- function(pCDFlist, sorted_pv, lambda = 0.05, pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_DBR_fast', PACKAGE = 'DiscreteFDR', pCDFlist, sorted_pv, lambda, pCDFcounts)
}

#' @rdname kernel
kernel_DBR_crit <- function(pCDFlist, support, sorted_pv, lambda = 0.05, alpha = 0.05, pCDFcounts = NULL) {
    .Call('_DiscreteFDR_kernel_DBR_crit', PACKAGE = 'DiscreteFDR', pCDFlist, support, sorted_pv, lambda, alpha, pCDFcounts)
}