R/pcutils-package.R

In pcutils: Some Useful Functions for Statistics and Visualization

#' @keywords internal
"_PACKAGE"

## usethis namespace: start
#' @importFrom utils data head download.file untar combn
#' @importFrom stats rnorm sd var na.omit setNames median quantile as.formula coef cor dist start end hclust lm model.frame chisq.test
#' @importFrom grDevices colorRampPalette png pdf dev.off
#' @importFrom graphics plot.new text legend hist par
#' @import dplyr
#' @import ggplot2
## usethis namespace: end
NULL

## quiets concerns of R CMD check re: the .'s that appear in pipelines
if (getRversion() >= "2.15.1") utils::globalVariables(c("."))

# Load the value of the option on package startup
.onAttach <- function(libname, pkgname) {
  if (!dir.exists(tools::R_user_dir("pcutils"))) dir.create(tools::R_user_dir("pcutils"), recursive = TRUE)
  refresh_config()
}

# read user config first.
refresh_config <- function() {
  if (file.exists(system.file("config", package = "pcutils"))) {
    default_options <- readRDS(file = system.file("config", package = "pcutils"))
  } else {
    default_options <- NULL
  }
  file_path <- file.path(tools::R_user_dir("pcutils"), "config")
  if (file.exists(file_path)) {
    options_to_load <- readRDS(file = file_path)
    if (length(options_to_load) == 0) options_to_load <- NULL
    inter <- intersect(names(options_to_load), names(default_options))
    la <- setdiff(names(default_options), inter)
    options_to_load <- append(default_options[la, drop = FALSE], options_to_load)
  } else {
    options_to_load <- default_options
  }
  # set options
  options("pcutils_config" = options_to_load)
}

#' Show config
#'
#' @return config
#' @export
show_pcutils_config <- function() {
  refresh_config()
  config <- getOption("pcutils_config")
  return(config)
}

#' Set config
#'
#' @param item item
#' @param value value
#'
#' @return No value
#' @export
#'
set_pcutils_config <- function(item, value) {
  refresh_config()
  config <- getOption("pcutils_config")
  if (is.null(value)) {
    config <- config[-which(names(config) == item)]
  } else {
    config <- pcutils::update_param(config, setNames(list(value), item))
  }
  saveRDS(config, file = file.path(tools::R_user_dir("pcutils"), "config"))
  options("pcutils_config" = config)
  message("Set sucessfully!")
}