R/bs_summary.R

In MikeKSmith/rspeaksnonmem: Read, Modify and run NONMEM from within R

#' Parses the PsN bootstrap results file (bootstrap_results.csv)
#'
#' @param fileName fileName for the bootstrap results file. Default
#' 'bootstrap_results.csv'
#' @param bs.dir Directory containing control stream and where bootstrap
#' results file (bootstrap_results.csv) is stored. Defaults to './bootstrap_dir1'
#' as PsN default.
#' @return list containing parsed blocks from bootstrap_results.csv
#' @examples
#'
bs_summary <- function(fileName = "bootstrap_results.csv",
                       working.dir = NULL) {

  # If the working.dir argument is populated then create a full file path
  # Otherwise assume that fileName argument is a full file path.
    if(!is.null(working.dir)) fileName <- file.path(working.dir, fileName)
    text <- readLines(fileName)

    diagnostics <- read.csv(fileName, skip = grep("^diagnostic", text), header = T,
        nrows = 1)[-1]

    means <- read.csv(fileName, skip = grep("^means", text) + 1, header = F, nrows = 1)[-1]
    names(means) <- gsub("\\s", "", read.csv(fileName, skip = grep("^means", text),
        nrows = 1, header = F, stringsAsFactors = F)[-1])

    bias <- read.csv(fileName, skip = grep("^bias", text) + 1, header = F, nrows = 1)[-1]
    names(bias) <- gsub("\\s", "", read.csv(fileName, skip = grep("^bias", text),
        nrows = 1, header = F, stringsAsFactors = F)[-1])

    se_CI <- read.csv(fileName, skip = grep("^standard.error.confidence", text) +
        1, nrows = 8, header = F, row.names = 1)
    names(se_CI) <- gsub("\\s", "", read.csv(fileName, skip = grep("^standard.error.confidence",
        text), nrows = 1, header = F, stringsAsFactors = F)[-1])
    row.names(se_CI) <- gsub("\\s", "", row.names(se_CI))

    se <- read.csv(fileName, skip = grep("^standard.error", text) + 1, header = F,
        nrows = 1)[-1]
    names(se) <- gsub("\\s", "", read.csv(fileName, skip = grep("^standard.error",
        text), nrows = 1, header = F, stringsAsFactors = F)[-1])

    medians <- read.csv(fileName, skip = grep("^medians", text) + 1, header = F,
        nrows = 1)[-1]
    names(medians) <- gsub("\\s", "", read.csv(fileName, skip = grep("^medians",
        text), nrows = 1, header = F, stringsAsFactors = F)[-1])

    perc_CI <- read.csv(fileName, skip = grep("^percentile", text) + 1, nrows = 8,
        header = F, row.names = 1)
    names(perc_CI) <- gsub("\\s", "", read.csv(fileName, skip = grep("^percentile",
        text), nrows = 1, header = F, stringsAsFactors = F)[-1])
    row.names(perc_CI) <- gsub("\\s", "", row.names(perc_CI))

    out <- list(diagnostics = diagnostics, means = means, bias = bias, se_CI = se_CI,
        se = se, medians = medians, perc_CI = perc_CI)
    out
}