In Lightbridge-KS/pkgtemp: Template for R Developer

knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(eval = FALSE)
here::i_am("dev/build.Rmd")
library(here)

How To

Essential Manuals and Packages:

• R Package Book
• usethis

I recommend initial setup by running the code that is not comment. Then, run the other commented code when you're ready.

Git

usethis::use_git()

Ignore

Git Ignore

Tell Git not to track theses:

usethis::use_git_ignore("/dev/") # (Optional) ignore `dev` folder at PKG root
# usethis::use_git_ignore("file") 

Build Ignore

Tell R not to build theses into R package:

usethis::use_build_ignore("dev") # (Require) if you use this template
# usethis::use_build_ignore("file")

Metadata

DESCRIPTION

usethis::use_description()

LICENSE

Use licence file by use_*_license() family of functions

usethis::use_mit_license() # MIT

User Doc

README

# usethis::use_readme_rmd()

Lifecycle badges

# usethis::use_lifecycle_badge("experimental")

Vignette

# usethis::use_vignette("PKG")

## Articles
# usethis::use_article()

NEWS

# usethis::use_news_md()

Dependencies

Imports

A recommended approach

# usethis::use_pipe() # If package use `%>%`
# usethis::use_tibble() # If package use `tbl_df` class

# usethis::use_package("pkg") 

## Developmental Package (not on CRAN)
# usethis::use_dev_package("pkg", remote = "OWNER/REPO")

Import from

Importing a function from another package allows you to refer to it without a namespace (e.g., fun() instead of package::fun()).

# usethis::use_import_from("rlang", ":=") # Must have if use `:=`

Suggests

Use suggested packages for example datasets, to run tests, build vignettes, or maybe there’s only one function that needs the package.

# usethis::use_package("pkg", type = "Suggests")

Functions

Write some R functions!

# usethis::use_r("fun1")
# usethis::use_test("fun1")

Testing

testthat

# usethis::use_testthat()

Helper function for testing can be place in tests/testthat/helper-tests.R

# fs::file_create(here("tests/testthat/helper-tests.R"))

Package Coverage (Local)

See covr

# covr::package_coverage()

for interactive use in viewer pane:

# covr::report()

Data

Exported Data

• usethis::use_data(): To store exported data in data/. Each file in this directory should be .rda file containing a single object.

• usethis::use_data_raw(): To store code that used for data preparation in data-raw/

# usethis::use_data(data1) 

# usethis::use_data_raw("data1") # Code to prepare data

Documenting datasets

Document the name of the dataset in R/ as roxygen2:

#' Prices of 50,000 round cut diamonds.
#'
#' A dataset containing the prices and other attributes of almost 54,000
#' diamonds.
#'
#' @format A data frame with 53940 rows and 10 variables:
#' \describe{
#'   \item{price}{price, in US dollars}
#'   \item{carat}{weight of the diamond, in carats}
#'   ...
#' }
#' @source \url{http://www.diamondse.info/}
"diamonds"

Internal Data

Save all of the objects for internal use in R/sysdata.rda.. They don’t need to be documented.

# usethis::use_data(int_data1, int_data2, internal = TRUE)

Raw Data

If you want to show examples of loading/parsing raw data, put the original files in inst/extdata.

# usethis::use_directory("inst/extdata")

## Write Raw Data
# readr::write_csv(mtcars, here("inst/extdata/mtcars.csv"))

Function: Get Path to Example Data

This function allows user to access paths to raw data.

Inspired from readr example.

# usethis::use_r("example") # Create `example.R` to store `PKG_example()`

• Copy this PKG_example() to example.R, replace PKG with your package name.

#' Get path to PKG example
#'
#' PKG comes bundled with a number of sample files in its `inst/extdata`
#' directory. This function make them easy to access
#'
#' @param file Name of file. If `NULL`, the example files will be listed.
#' @export
#' @examples
#' library(PKG)
#' PKG_example()
#' PKG_example("file.csv")
PKG_example <- function(file = NULL) {

  if (is.null(file)) {
    dir(system.file("extdata", package = "PKG"))

  } else {
    system.file("extdata", file, package = "PKG", mustWork = TRUE)
  }

}

Template

Add an R Markdown Template

# usethis::use_rmarkdown_template(
#   template_name = "Template Name",
#   template_dir = "dir-name",
#   template_description = "A description of the template",
#   template_create_dir = FALSE
# )

See also:

• Create Rmd Templates

Global Var

If R CMD Check shows a message like:

Undefined global functions or variables:
  var1 var2

Put this:

# Declare global variables 
if(getRversion() >= "2.15.1")  utils::globalVariables(c("var1", "var2"))

in the same file as where you have package-level documentation.

# usethis::use_package_doc()

See this Discussion

CI workflow

Github action to automate R Package workflow.

Learn more

R-CMD-check

Github action to run R CMD Check in the cloud.

This will

1. Create a YAML file: .github/workflows/R-CMD-check.yaml

2. Adding R-CMD-check badge to 'README.Rmd'

## Quickstart CI workflow
# usethis::use_github_action_check_release()

Ref: Quickstart WF

Test Coverage

1. Call usethis::use_coverage()

# usethis::use_coverage()

1. Use github action test-coverage

This will connect your package to codecov.

# usethis::use_github_action("test-coverage")

Ref: test coverage WF

1. Click on codecov badge in README, it will open codecov site, then copy token to clip board, and paste the token and run:

# covr::codecov(token = "your-token")

Lightbridge-KS/pkgtemp documentation built on May 10, 2022, 7:33 p.m.