R/compile.manuscript.r

In janejkanske/SupaLarna: Package for the SuperLearner vs clincians study

#' Compile manuscript function
#'
#' This function compiles the Superlearner vs clinicians manuscript
#' @param manuscript_file_name_prefix The file name prefix of the manuscript as a character vector of length 1. No default.
#' @param results_path The path to the results list rds object. Defaults to "./". 
#' @param manuscript_file_format The format of the manuscript file. Defaults to "rtex".
#' @param compiler The compiler to use when compiling the rtex manuscript into a pdf. Defaults to pdflatex.
#' @export
compile.manuscript <- function(
                               manuscript_file_name_prefix,
                               results_path = "./",
                               manuscript_file_format = "rtex",
                               compiler = "pdflatex"
                               )
{
    ## Error handling
    results_file <- paste0(results_path, "results.rds")
    if (!file.exists(results_file)) stop ("No results list rds exist in that path")
    ## Get results list
    results_list <- readRDS(results_file)
    ## Attached results list
    attach(results_list)
    ## Get list of files matching the manuscript file name prefix
    files <- list.files(pattern = paste0("^", manuscript_file_name_prefix))
    manuscript_file <- grep(paste0(manuscript_file_format, "$"), files, value = TRUE)
    if (length(manuscript_file) > 1) stop("There are more than 1 file matching both prefix and format. Maybe there are several manuscript versions in this directory?")
    ## Compile manuscript using knit2pdf
    knit2pdf(manuscript_file, compiler = compiler)
}