R/add_make_all.R

In kabagg/moffitt2018: Tools for Structuring Files (Title Case)

#' Add MAKE ALL script
#'
#' Adds 99_make_clean.R to R/, and defines files
#' to be autogenerated. Currently defaults running
#' all prefix-numbered files up to 89 (files in the
#' 90's are assumed to be infrastructure, not analyses).
#'
#' @return adds 99_make_all.R to R/ if this doesn't
#'   already exist.
#' @import here
#' @export
add_make_all <- function(){

  if(file.exists(here::here("R", "99_make_all.R"))){
    cat("R/99_make_all.R already exists!\n")
  }else{
    file.create(here::here("R", "99_make_all.R"))
    files_in_r <- dir(here::here("R"))
    numbered_files <-
      files_in_r[grep("^[[:digit:]]{2}_", files_in_r)]
    files_in_r_to_run <-
      numbered_files[grep("[0-8]",
                          substr(numbered_files, 1, 1))]

    file_string <- "files_in_r_to_run <- \n  c("
    if(length(files_in_r_to_run) > 0){
      for(i1 in 1:length(files_in_r_to_run)){
        file_string <-
          paste0(file_string, "\"",
                 files_in_r_to_run[i1], "\"")
        if(i1 < length(files_in_r_to_run)){
          file_string <- paste0(file_string, ",\n    ")
        }
      }
    }
    file_string <- paste0(file_string, ")")

    writeLines(
      c("library(here)",
        "library(rmarkdown)",
        "",
        "if(!dir.exists(here::here(\"results\"))){",
        "  dir.create(here::here(\"results\"))",
        "}",
        "",
        file_string,
        "",
        "if(length(files_in_r_to_run) > 0){",
        "",
        "  for(i1 in 1:length(files_in_r_to_run)){",
        "    rmarkdown::render(here::here(\"R\", files_in_r_to_run[i1]),",
        "      output_format =",
        "        github_document(html_preview = TRUE,",
        "          toc = TRUE),",
        "      output_dir = here::here(\"results\"))",
        "",
        "  }",
        "}",
        "",
        "if(file.exists(here::here(\"README.Rmd\"))){",
        "  rmarkdown::render(here::here(\"README.Rmd\"),",
        "    output_format =",
        "      github_document(html_preview = TRUE,",
        "        toc = TRUE),",
        "    output_dir = here::here())",
        "}"),

      con = here::here("R", "99_make_all.R")
    )
  }

}