R/set_posterior.R

In richelbilderbeek/wiritttes: WIRITTE simulation

#' Set a BEAST2 posterior of a file
#' @param file A loaded parameter file
#' @param i the index of the posterior
#' @param posterior a BEAST2 posterior, may also be NA
#' @return the modified file
#' @export
#' @author Richel Bilderbeek
set_posterior_by_index <- function(file, i, posterior) {
  if (i < 1) {
    stop("index must be at least 1")
  }
  if (i > length(file$posteriors)) {
    stop("index must be less than number of posteriors")
  }
  file$posteriors[[i]] <- list(posterior)
  file
}

#' Set an posterior to a file
#' @param file A loaded parameter file
#' @param sti the species tree index, a value from 1 to and including 2
#' @param ai the alignment index,
#'   the ai-th alignment of that species tree,
#'   a value from 1 to and including
#'   the number of alignments per species tree
#' @param pi the posterior index,
#'   the pi-th posterior of that alignment,
#'   a value from 1 to and including
#'   the number of posteriors per alignment
#' @param posterior a posterior, may also be NA
#' @return the modified file
#' @export
#' @author Richel Bilderbeek
set_posterior <- function(
  file, sti, ai, pi, posterior
) {
  if (sti < 1) {
    stop("sti must be at least 1")
  }
  if (sti > 2) {
    stop("sti must at most be 2")
  }
  if (ai < 1) {
    stop("ai must be at least 1")
  }
  napst <- wiritttes::extract_napst(file = file)
  if (ai > napst) {
    stop("ai must at most be napst")
  }
  if (pi < 1) {
    stop("pi must be at least 1")
  }
  nppa <- wiritttes::extract_nppa(file = file)
  if (pi > nppa) {
    stop("pi must at most be nppa")
  }
  if (!tracerer::is_posterior(posterior)) {
    stop("posterior must be a posterior")
  }
  nstpist <- 2 # Number species trees per incipient species tree
  i <- p2i(sti = sti, pi = pi, ai = ai, nstpist = nstpist, napst = napst, nppa = nppa) # nolint

  return(
    set_posterior_by_index(
      file = file,
      i = i,
      posterior = posterior
    )
  )
}