R/create_readme.R

In farhadsalimi/registryr: Functions for the Clinical Registries Analyses

#' Create ReadMe.md files
#'
#' This function creates ReadMe.md in the CORRP templates for the standard
#' file structure
#'
#'@param template Which ReadMe.md files should be created? Default is all. Partial
#'matching does work.
#'@param path Where should they be created? Default is the working directory.
#'@return
#'This function creates the desired readme files. It will not overwrite the file
#'however if it does not exists. It does not return anything.
#'@keywords ReadMe ReadMe.md
#'@export
create_readme <- function(template = c('assets', 'rmds', 'raw_data',
                                      'produced_data', 'plots', 'tables',
                                      'reports', 'functions', 'rscripts', 'adhoc_req'),
                          path = getwd()){
  # set which ReadMe.md files to create
  template <- match.arg(template, several.ok = T)

  # create list with lines for each template
  readme <- list()

  readme$assets <- c("# Assets  ",
                    "  ",
                    "This folder contains the scope of work and other relevant files (e.g data dictionary, feedback, minutes, etc).  ",
                    "  ",
                    "Details about the files:  ",
                    "  ",
                    "File | Description",
                    "---|---------------------------------------------------------------------",
                    "  ",
                    "")
  readme$plots <- c("# Plots  ",
                         "  ",
                         "This folder contains all the plots.  ",
                         "  ",
                         "Details about the files:  ",
                         "  ",
                         "Folder | Description",
                         "---|---------------------------------------------------------------------",
                         "  ")
  readme$rmds <- c("This folder contains all the rmarkdown files  ",
                   "  ",
                   "Details about the files in this folder:",
                   "  ",
                   "File | Description",
                   "---|---------------------------------------------------------------------",
                   "  ")
  readme$produced_data <- c("# Produced Data  ",
                            "  ",
                            "Scripts that created the files in this folder:  ",
                            "  ",
                            "File | Script | Description",
                            "---|------------------|---------------------------------------------------",
                            "  ")
  readme$raw_data <- c("# Raw Data",
                      "  ",
                      "Details about the files:  ",
                      "  ",
                      "File | Details",
                      "---|---------------------------------------------------------------------",
                      "    ",
                      "  ")

  readme$tables <- c("# Tables",
                            "  ",
                            "This folder contains all the tables.  ",
                            "  ",
                            "Details about the files:  ",
                            "  ",
                            "Folder | Description",
                            "---|---------------------------------------------------------------------",
                            "  ",
                            "  ")
  readme$reports <- c("# Reports",
                      "  ",
                      "This folder contains the reports generated by rmd files.  ",
                      "  ",
                      "Details about the files:  ",
                      "  ",
                      "File | Description",
                      "---|---------------------------------------------------------------------",
                      "  ")

  readme$functions <- c("# Functions",
                      "  ",
                      "This folder contains R files with functions only they need to be sourced from another script.  ",
                      "  ",
                      "Details about the files:  ",
                      "  ",
                      "File | Description",
                      "---|---------------------------------------------------------------------",
                      "  ")

  readme$rscripts <- c("# Rscripts",
                        "  ",
                        "This folder contains the scripts in R, mainly used when there is too much code to fit in a R markdown. ",
                        "  ",
                        "Details about the files:  ",
                        "  ",
                        "File | Description",
                        "---|---------------------------------------------------------------------",
                        "  ")

  readme$adhoc_req <- c("# Ad-hoc requests",
                       "  ",
                       "This folder contains the files (scripts, rmds, etc) that are not related to the main aims of the project. ",
                       "  ",
                       "Details about the files:  ",
                       "  ",
                       "File | Description",
                       "---|---------------------------------------------------------------------",
                       "  ")

  # Function for creating the directory
  createDir <- function(x){
    paste0(path, '/', x)
  }

  createFiles <- function(x){
    file.path(path, paste0(x, '/ReadMe.md'))
  }

  readme <- readme[template]

  pathnames <- sapply(names(readme), createDir)
  dir_created <- lapply(pathnames, dir.create, showWarnings = F, recursive = T)
  con <- lapply(names(readme), createFiles)
  doNotOverwrite <- sapply(con, file.exists)
  readme <- readme[!doNotOverwrite]
  con <- con[!doNotOverwrite]
  files_created <- mapply(writeLines, lapply(readme, paste0, collapse = '\n'), con)
}