R/cctu_initialise.R

In shug0131/cctu: In-House Functions for Report Writing at Cambridge Clinical Trials Unit

#' initialise  objects for using cctu package
#'
#' @param root the root directory to start in
#' @param scripts logical create the standard set of scripts. Intended to be
#' used once interactively at the start of coding for an analysis.
#' @param rm logical whether to also run \code{\link{rm_output}} with its
#' default values, to delete all the files in the output directory.
#' @param description logical,  whether to create a DESCRIPTION file if one does not exist.
#' @param output character string giving the name of the output folder. Can be
#' overriden by setting the option("cctu_output").
#' @return cctu_initialise gives an invisible return of logical indicating if
#' the directories have been created. The directories needed are "Output", and
#' within "Output", "Core", "Figures", "Reports".
#' It also runs \code{reset_code_tree(root)} automatically.
#'
#' @seealso \code{\link{dir.create}} \code{\link{reset_code_tree}}
#'
#' @export
#' @importFrom magrittr %>% %<>%

#' @describeIn cctu_initialise create the standard directories for outputs
#'  if needed.
cctu_initialise <- function(root = getwd(), scripts = FALSE, rm = FALSE,
                            description = TRUE,
                            output = getOption("cctu_output",
                              default = "Output"
                            )) {
  root <- root %>% normalizePath()
  # root_slash <- root %>% final_slash()
  reset_code_tree(root_file = file.path(root, "ROOT"))
  if (!cctu_check_dir(root = root)) {
    dir.create(file.path(root, output)) &
      dir.create(file.path(root, output, "Core")) &
      dir.create(file.path(root, output, "Figures")) &
      dir.create(file.path(root, output, "Reports"))
  }
  if (scripts) {
    file.copy(
      system.file(file.path("scripts", "main.R"), package = "cctu"),
      root
    )
    file.copy(system.file(file.path("scripts", "Progs"), package = "cctu"),
      root,
      recursive = TRUE
    )
    dir.create(file.path(root, "library"))
    print("Maybe set up a Project in Rstudio and a git repository?\nCopy across or install packages in the project library, set .libPaths()?")
  }

  if (!file.exists("DESCRIPTION")) {
    if (description) {
      usethis::use_description(fields = list(Imports = "tidyverse,\n    eudract,\n    consort"))
      message("Edit DESCRIPTION Imports: to add the packages you want to load.\nUse  library_description()  to load them all automatically")
    } else {
      warning("Recommend to create and edit a DESCRIPTION file")
    }
  }


  if (rm) {
    rm_output()
  }
}


# spelling variant
#' @describeIn cctu_initialise identifical function with American spelling
#' @export
cctu_initialize <- cctu_initialise


#' @describeIn cctu_initialise Check if the directories exist for cctu
#' @param warnings logical indicator to issue warning if the directories do not
#' exist. Default FALSE.
#' @return cctu_check_dir gives a logical indicating if the directories exist,
#' @export

cctu_check_dir <- function(root = getwd(), warnings = FALSE,
                           output = getOption("cctu_output",
                             default = "Output"
                           )) {
  root <- normalizePath(root) # %>% final_slash
  check <- dir.exists(file.path(root, output)) &
    dir.exists(file.path(root, output, "Core")) &
    dir.exists(file.path(root, output, "Figures")) &
    dir.exists(file.path(root, output, "Reports"))
  if (warnings && !check) {
    warning("Default directories needed by cctu do not exist")
  }
  check
}



#' @describeIn cctu_initialise function to clear previous output files, but
#' leaves the directories in place
#'
#' @param core logical delete the files in /Core
#' @param figures logical delete the files /Figures
#' @param reports logical delete the files in /Reports
#' @param top logical delete top level files that are not in core/figures/reports.
#' @export



rm_output <- function(output = getOption("cctu_output", default = "Output"),
                      core = TRUE, figures = TRUE, reports = TRUE, top = TRUE) {
  if (top) {
    files <- list.files(output, recursive = FALSE)
    dirs <- list.dirs(output)[-1]
    dirs <- gsub(paste0(output, "/"), "", dirs)
    for (file in files) {
      if (!(file %in% c("Core", "Figures", "Reports", dirs))) {
        file.remove(file.path(output, file))
      }
    }
  }

  if (core) {
    files <- list.files(file.path(output, "Core"))
    for (file in files) {
      file.remove(file.path(output, "Core", file))
    }
  }
  if (figures) {
    files <- list.files(file.path(output, "Figures"))
    for (file in files) {
      print(file)
      file.remove(file.path(output, "Figures", file))
    }
  }
  if (reports) {
    files <- list.files(file.path(output, "Reports"))
    for (file in files) {
      file.remove(file.path(output, "Reports", file))
    }
  }
}