Function: set up raw data directory with a template data_processing.R

[mianzg]

Please test and review the following code and file @margauxgo

R/setup_rawdata.R inst/templates/data_processing.R

[mianzg]

We may refer to tests in usethis package to write our own tests: https://github.com/r-lib/usethis/tree/main/tests/testthat

[margauxgo]

@mianzg In the DESCRIPTION file, please align the 'Description' text with the rest of the text above. After that, I should be able to install the package from GitHub. Please also edit the workflow 'Data repository set-up' -> 3. -> v. devtools::install_github("openwashdata-dev/washr")

[margauxgo]

@mianzg Here is the template I like to use for data_processing.R:

# Description -------------------------------------------------------------
# R script to process uploaded raw data into a tidy, analysis-ready data frame
# Load packages -----------------------------------------------------------
library(tidyverse)
library(openwashdata)
library(readxl)
library(janitor)
library(dplyr)

# Read data -------------------------------------------------------------
data_in <- read_csv("data-raw/dataset.csv") |>
  as_tibble()
codebook <- read_excel("data-raw/codebook.xlsx") |>
  clean_names()

# Tidy data ---------------------------------------------------------------

# Write data -------------------------------------------------------------
usethis::use_data(dataset, overwrite = TRUE)
fs::dir_create(here::here("inst", "extdata"))
write_csv(dataset, here::here("inst", "extdata", "dataset.csv"))
openxlsx::write.xlsx(dataset, here::here("inst", "extdata", "dataset.xlsx"))

[mianzg]

Thanks! I incorporate it into the template here https://github.com/openwashdata-dev/washr/pull/1/commits/9bd9158bb64f2ae41cd58b45482be42fab35e237

The "Read data" part are in comments to be as a suggestion.

Please also review the function update_description, which you may need to reinstall the package with devtools::install_github("openwashdata-dev/washr@dev")

[margauxgo]

@mianzg

• Concerning the setup_rawdata.R file, I would just change the documentation to

  #' Create the data-raw directory with a data-processing.R template
  #'
  #' @description
  #' `setup_rawdata()` creates a directory for raw data and provides an example script
  #' named `data_processing.R` for importing, processing and exporting the data. When running this function, 
  #' you may be prompted to override an existing `data_processing.R` file, which is initially 
  #' generated as empty. It's recommended to choose to override it, especially for openwashdata 
  #' dataset package development. The template assumes that the dataset name is the same as 
  #' the data package name.
  #'
  #' @export
  #'
  #' @examples
  #' \dontrun{
  #' setup_rawdata()
  #' # When prompted, select "yes" or a similar option to override the data_processing.R file
  #' }
  #'

• As for the update_description.R file, I would modify the documentation to

  #' Update the default DESCRIPTION to adhere to openwashdata style
  #'
  #' @description
  #' This function updates the DESCRIPTION file of an R package to comply with openwashdata standards.
  #' It adds or modifies fields such as doculicense, language, date, URL, etc.
  #'
  #' @param file File path to the R package containing the DESCRIPTION file. Defaults to the current working directory.
  #' @param github_user URL path to the GitHub user or organization hosting the package. Defaults to https://github.com/openwashdata.
  #'
  #' @export
  #'
  #' @examples
  #' \dontrun{
  #' update_description()
  #' }
  #'

  Concerning the testing of the functions, please have a look at the test_setup_rawdata.R and test_update_description.R files I just created, which are located in the tests/testthat directory. Everything seems to be working correctly! 😊

[mianzg]

@mianzg

• Concerning the setup_rawdata.R file, I would just change the documentation to

#' Create the data-raw directory with a data-processing.R template
#'
#' @description
#' `setup_rawdata()` creates a directory for raw data and provides an example script
#' named `data_processing.R` for importing, processing and exporting the data. When running this function, 
#' you may be prompted to override an existing `data_processing.R` file, which is initially 
#' generated as empty. It's recommended to choose to override it, especially for openwashdata 
#' dataset package development. The template assumes that the dataset name is the same as 
#' the data package name.
#'
#' @export
#'
#' @examples
#' \dontrun{
#' setup_rawdata()
#' # When prompted, select "yes" or a similar option to override the data_processing.R file
#' }
#'

• As for the update_description.R file, I would modify the documentation to

#' Update the default DESCRIPTION to adhere to openwashdata style
#'
#' @description
#' This function updates the DESCRIPTION file of an R package to comply with openwashdata standards.
#' It adds or modifies fields such as doculicense, language, date, URL, etc.
#'
#' @param file File path to the R package containing the DESCRIPTION file. Defaults to the current working directory.
#' @param github_user URL path to the GitHub user or organization hosting the package. Defaults to https://github.com/openwashdata.
#'
#' @export
#'
#' @examples
#' \dontrun{
#' update_description()
#' }
#'

Concerning the testing of the functions, please have a look at the test_setup_rawdata.R and test_update_description.R files I just created, which are located in the tests/testthat directory. Everything seems to be working correctly! 😊

I added the suggestions! For documentation suggestion, I think you can directly make the changes on the files and commit them and do not need to ask for my review

[mianzg]

For the tests, I borrowed the code from usethis so it creates a temporary package before running into the tests. The code is in tests/testthat/helper.R, which follows usethis package structure too.

With this, we can actually test on stuff expected on the created data package instead of the washr package. For instance, the test_setup_rawdata() is changed into:

options(usethis.quiet = TRUE)
test_that("File and directory are created", {
  create_local_package() # Create a temporary pkg

  rlang::local_interactive(FALSE) #Disable interactive R
  print(getwd())
  washr::setup_rawdata()
  expect_true(file.exists("data-raw/data_processing.R"))
})
unlink("data-raw", recursive = TRUE)

We deleted the tests on checking file size because the name of the data package varies and thus the generated file will have different sizes.