simtrial: Clinical Trial Simulation

#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
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#
#  This file is part of the simtrial program.
#
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#' MaxCombo p-value
#'
#' Computes p-values for the MaxCombo test based on output from [fh_weight()].
#' This is still in an experimental stage and is intended for use with
#' the [sim_fixed_n()] trial simulation routine.
#' However, it can also be used to analyze clinical trial data such as
#' that provided in the ADaM ADTTE format.
#'
#' @param z A dataset output from [fh_weight()]; see examples.
#' @param algorithm This is passed directly to the `algorithm` argument
#'   in [mvtnorm::pmvnorm()].
#'
#' @return A numeric p-value.
#'
#' @importFrom mvtnorm pmvnorm GenzBretz
#' @noRd
pvalue_maxcombo <- function(
    z,
    algorithm = mvtnorm::GenzBretz(maxpts = 50000, abseps = 0.00001)) {
  zmin <- as.numeric(min(z$z))
  lower_limits <- rep.int(zmin, times = nrow(z))

  correlation_matrix <- z[, grep("^v", colnames(z))]
  correlation_matrix <- data.matrix(correlation_matrix)

  distribution <- mvtnorm::pmvnorm(
    lower = lower_limits,
    corr = correlation_matrix,
    algorithm = algorithm
  )

  ans <- 1 - distribution[1]

  as.numeric(ans)
}