R/save_lml_logs.R

In rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm

#' save_lml_logs
#'
#' Saves the log marginal likelihoods to a text file.
#'
#'
#' @param hb.object The resulting object from runnign hierBAPS
#' @param file The file you would like to save the log output to.
#'
#' @examples
#' snp.matrix <- load_fasta(system.file("extdata", "small_seqs.fa", package = "rhierbaps"))
#' hb.result <- hierBAPS(snp.matrix, max.depth=2, n.pops=20)
#' save_lml_logs(hb.result,  file.path(tempdir(), "output_file.txt"))
#'
#' @export
save_lml_logs <- function(hb.object, file){

  if (!is.character(file)) stop("Invalid file name. Must be a valid string.")
  if ((!is.list(hb.object) || !is.data.frame(hb.object$partition.df)
       ) || !is.list(hb.object$lml.list)) stop("Invalid hb.object!")

  sink(file)
  for(i in 1:length(hb.object$lml.list)){
    cat(names(hb.object$lml.list)[[i]], "\n")
    cat("cluster names:\t", paste(names(hb.object$lml.list[[i]]), collapse = "\t"), "\n")
    cat("cluster log marginal likelihood:\t", paste(hb.object$lml.list[[i]], collapse = "\t"), "\n")
  }
  sink()
}