Helpers for writing R-packages

rpackages-helpers.md

Helpers for writing R-packages

Links

Helpful links for developing R packages

• rodev package (usethis like)
• Writing an R package from scratch (with usethis)
• usethis package workflow by Emil Hvitfeldt
• Sharla's post on usethis
• R packages by Hadley Wickham
• usethis
• rOpenSci packaging guide
• Packages for testing your R-Packages by Locke Data
• Cheatsheet
• Other resources (by Karl Broman)
• continuous integration (but with gitlab)

Workflow

1. Cmd + Alt + Shift + R to insert skeleton
2. Cmd + Shift + L or devtools::load_all(): loads package
3. Cmd + Shift + D: documents
4. Cmd + Shift + B: builds
5. Cmd + Shift + T or devtools::test(): runs tests
6. devtools::build_vignettes()
7. Cmd + Shift + E or devtools::check(): Runs R CMD check + some additional stuff
8. goodpractice::gp()

Workflow

• inspired by seabbs package.
• create a file called data-raw/create-package.R:

#install.packages("devtools")
#install.packages("usethis")

usethis::use_description(fields = list(Title = "ggplot2 Extensions for Plotting GWAS Summary Statistics",
                                       `Authors@R` = 'person("Sina", "Rüeger",
                                       email = "[email protected]",
                                       role = c("aut", "cre"))',
                                       Description = "Provides Manhattan plot and QQplot as a ggplot2 extension. For high-dimensional GWAS data there is a hex version of the QQplot (which is more of a diagnostics tool)."))

usethis::use_github_links()
usethis::use_version(which = "minor") ## "major", "minor", "patch", "dev"

# initial setup
usethis::use_data_raw()
#usethis::use_cran_badge()
usethis::use_mit_license("Sina Rüeger")
usethis::use_readme_rmd()

## create `testthat` folder
usethis::use_testthat()

## add Roxygen into description file
usethis::use_roxygen_md()

## Suggest & Imports
## adds suggests and imports to DESCRIPTION
usethis::use_package("ggplot2", type = "Import", min_version = "3.1.0" )
usethis::use_package("dplyr", type = "Import", min_version = "0.7.8" )
usethis::use_package("scales", type = "Import", min_version = "1.0.0" )
usethis::use_package("hexbin", type = "Import", min_version = "1.27.2" )

usethis::use_package("ggrastr", type = "Suggests", min_version = "0.1.7" )
usethis::use_package("GWAS.utils", type = "Suggests", min_version = "0.0.0.9000" )
usethis::use_package("skimr", type = "Suggests" )
usethis::use_package("plyr", type = "Suggests", min_version = "1.8.4" )
usethis::use_package("wesanderson", type = "Suggests", min_version = "0.3.6" )
usethis::use_package("vctrs", type = "Suggests", min_version = "0.1.0" )
usethis::use_package("knitr", type = "Suggests", min_version = "0.1.7" )
usethis::use_package("rmarkdown", type = "Suggests")
usethis::use_package("qqman", type = "Suggests")

usethis::use_pipe()

#Vignettes
usethis::use_vignette("gggwas-reasoning", "ggGWAS reasoning" )
usethis::use_vignette("gggwas-internals", "ggGWAS internals")

##Build site, and make pkgdown
devtools::document()
devtools::build_vignettes()
devtools::build()
usethis::use_package_doc()
codemetar::write_codemeta()

## run examples
devtools::run_examples()

Helpers

1. devtools::use_package(): adds suggests and imports to DESCRIPTION
2. devtools::use_testthat(): creates testthat folder
3. usethis::use_test("opensnp"): creates a new test
4. usethis::use_package_doc(): toplevel package doc
5. devtools::run_examples(pkg = ".", "stat_gwas_qq.Rd")
6. usethis::use_data(yourdata): to export data
7. usethis::use_r(): create new R file
8. usethis::ui_done("Report saved to {usethis::ui_path(out_path)}")

For vignettes, first run usethis::use_vignette("my-vignette") then devtools::build_vignettes(). Also useful: devtools::install(build_vignettes = TRUE).

Tagging

Version: major.minor.patch.dev, where dev is at least 9000.

1. $ git tag -a v0.1 -m "<message>"
2. $ git push origin v0.1

Misc

Occasionally mark all code and run

• Cmd + I for indenting
• Cmd + Shift + A for reformatting (spaces etc.)
• usethis::use_tidy_style() (see styler package)
• (or run the styler package options in the addins menu, but they will undo some of the stuff from reformatting before)