R/efftox_superiority.R

In brockk/trialr: Clinical Trial Designs in 'rstan'

#' @title Get dose-superiority matrix in EffTox
#'
#' @description Get a dose-superiority matrix from an EffTox dose analysis.
#' EffTox seeks to choose the dose with the highest utility, thus superiority
#' is inferred by posterior utility. The item in row i, col j is the posterior
#' probability that the utility of dose j exceeds that of dose i.
#'
#' @param fit An instance of \code{efftox_fit}.
#'
#' @return n by n matrix, where n is number of doses under investigation.
#' The item in row i, col j is the posterior probability that the utility of
#' dose j exceeds that of dose i.
#'
#' @export
#'
#' @examples
#' fit <- stan_efftox_demo('1N 2E 3B')
#' sup_mat <- efftox_superiority(fit)
efftox_superiority <- function(fit) {
  u <- rstan::extract(fit$fit, par = 'utility')[[1]]
  superiority_mat <- sapply(1:ncol(u), function(i) sapply(1:ncol(u), function(j)
    mean(u[ , i] > u[ , j])))
  diag(superiority_mat) <- NA
  dimnames(superiority_mat) = list(1:ncol(u), 1:ncol(u))
  return(superiority_mat)
}