How to improve your R package

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# How to improve your R package
## Automatically ✨, and not 🧠
### Maëlle Salmon – e-Rum 2020
### 
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</svg> <a href="https://maelle.github.io/erum2020/index.html#1">tiny.cc/erum2020</a> 
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</svg> <a href="https://masalmon.eu">masalmon.eu</a> 
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</svg> ma_salmon 
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</svg> maelle 
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</svg> <a href="https://www.pexels.com/photo/brown-cardboard-close-up-corrugated-479450/">icon0.com on Pexels</a>

---

# Ciao!

* Work: rOpenSci, R-hub (🙏 R Consortium)

* Volunteering: rOpenSci, R-Ladies, R Weekly

---

# Developing packages is great

* For (future) you,

* The collaborators you know,

* And the collaborators you don't.

.small[Picture by [cottonbro](https://www.pexels.com/photo/person-holding-a-pink-ribbon-3927232/)]

---

# Package development from 0 to hero?

Easier with modern tools.

Online [tutorials](https://masalmon.eu/2017/12/11/goodrpackages/#short-tutorials), [R packages book by Hadley Wickham and Jenny Bryan](https://r-pkgs.org/).

... Now what?!

* Automatic tools & how to use them;

* Making the most of information out there.

Pick one or a few tip(s)!

---

class: part-slide, center, bottom
background-image:url(img/girl-in-green-shirt-lying-on-brown-leather-couch-4107241.jpg)

#     Workflow automation tools

[_cottonbro on Pexels_](https://www.pexels.com/photo/girl-in-green-shirt-lying-on-brown-leather-couch-4107241/)

---

# Assessing your package

* [R CMD check or `devtools::check()`](http://r-pkgs.org/check.html)

* [`BiocCheck`](https://bioconductor.org/packages/release/bioc/html/BiocCheck.html)

* [`goodpractice`](http://mangothecat.github.io/goodpractice/) and [`lintr`](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/) (possibly via [CodeFactor](https://www.codefactor.io)).

* [`covr::package_coverage()`](http://covr.r-lib.org/reference/package_coverage.html)

* [`devtools::spell_check()`](http://devtools.r-lib.org/reference/spell_check.html)

---

# Improve metrics by hand?!

Yes and no!

.small[Picture by [Lisa Fotios](https://www.pexels.com/photo/yellow-latex-gloves-on-dish-rack-4039452/)]
---

# Tools for improving

* [`styler`](https://styler.r-lib.org/). Better paired with [version control](https://happygitwithr.com/).

* [`roxygen2`](https://roxygen2.r-lib.org/articles/rd.html) NAMESPACE generation. Switching: [`Rd2roxygen`](https://yihui.org/rd2roxygen/).

* [`pkgdown`](https://pkgdown.r-lib.org/). Work on reference index & navbar!

* `usethis` e.g. [`usethis::use_test()`](https://usethis.r-lib.org/reference/index.html#section-package-development).

---

# When and where to use the tools?

Right after my talk (not now 😜), but then?

.small[Picture by [Bich Tran](https://www.pexels.com/photo/photo-of-planner-and-writing-materials-760710/)]

---

# Continuous integration

**Run something every time you make a change**

> "The idea behind continuous integration is that CI will automatically run R CMD check (along with your tests, etc.) every time you push a commit to GitHub. You don't have to remember to do this; CI automatically checks the code after every commit."
[Julia Silge](https://juliasilge.com/blog/beginners-guide-to-travis/)

Travis, GitHub Actions, Circle CI, [`tic` package](https://docs.ropensci.org/tic/)...

---

# Continuous integration

How to learn?

[Julia Silge's post](https://juliasilge.com/blog/beginners-guide-to-travis/) - [Jim Hester's GitHub Actions talk](https://www.jimhester.com/talk/2020-rsc-github-actions/) - [`usethis` helpers](https://usethis.r-lib.org/reference/index.html#section-continuous-integration)

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">LIFE HACK: My go-to strategy for getting Travis builds to work is snooping on *other* people&#39;s .travis.yml files. Shoutout today to the tidyr .travis.yml for solving my problem! <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> 🙌</p>&mdash; Julia Silge (@juliasilge) <a href="https://twitter.com/juliasilge/status/1205183124868681728?ref_src=twsrc%5Etfw">December 12, 2019</a></blockquote>

---

# More with continuous integration

Couple a thing (R CMD check? pkgdown site building?) to

... each commit,

... every Monday,

... applying a label to a pull request?

---

# Pre-commit

.small[Illustration by [Mara Averick](https://twitter.com/dataandme/status/1255510799273132032)]

---

# Pre-commit

[`precommit` R package](https://lorenzwalthert.github.io/precommit/) -- Python [precommit framework](https://pre-commit.com/)

* Setup hooks

* Hooks for styling, parsable R code, spell checks, etc.

.small[Picture by [Castorly Stock](https://www.pexels.com/photo/person-holding-purple-crochet-hook-and-white-yarn-3945638/)]

---

# Check things before show time

CRAN release! 🐉 Checks on different platforms, URLs, spell checks...

* [submission checklist](https://cran.r-project.org/web/packages/submission_checklist.html)

* [`usethis::use_release_issue()`](https://usethis.r-lib.org/reference/use_release_issue.html) creating a GitHub issue with important items.

* [`devtools::release()` function](https://github.com/r-lib/devtools/blob/b166195be72927a003e6937de5c3239881095a9f/R/release.R#L39)

---

# Improve workflow vs. procrastinate

Risk of spending too much time on [meta-work](https://youtu.be/dIjKJjzRX_E?t=633).

.small[Picture by [Pedro da Silva](https://unsplash.com/photos/unEmGQqdO7Q)]

---

class: part-slide, center, bottom
background-image:url(img/man-in-gray-dress-shirt-sitting-on-red-leather-sofa-chair-4107239.jpg)

#     Reading code & about code

[_cottonbro on Pexels_](https://www.pexels.com/photo/man-in-gray-dress-shirt-sitting-on-red-leather-sofa-chair-reading-book-4107239/)

---

# Why read source code

* You want to know what is going on.

* You want to build on the function/package for your own goals.

* You're just curious.

* You need examples of a thing in the wild.

---

# How to read source code

* [`lookup` package](https://github.com/jimhester/lookup#readme)

* [GitHub search](https://help.github.com/en/articles/about-searching-on-github)

* Mirrors of [CRAN packages](https://github.com/cran) and [R-source](https://github.com/wch/r-source), on GitHub.

.small[Picture by [Sereja Ris](https://unsplash.com/photos/g3B53PbBfwU)]

---

# Reading code...

And trying things out!

Fork, clone, and explore!

[Podcast episode "Learning a new codebase", with Patricia Aas](https://www.allthingsgit.com/episodes/learning_a_new_codebase_with_patricia_aas.html)

.small[Picture by [Dimitri Houtteman](https://unsplash.com/photos/93AcQpzcASE)]

---

# Read blogs and fora

Blog posts: digested information.

* [R-hub blog](https://blog.r-hub.io/), rOpenSci [blog](https://ropensci.org/blog) and [tech notes](https://ropensci.org/technotes)

* [tidyverse blog](https://www.tidyverse.org/blog/2020/04/self-cleaning-test-fixtures/)

* [R Weekly](https://rweekly.org/)

* _Your_ blog?

Fora: Help and learn.

[R-package-devel](https://stat.ethz.ch/mailman/listinfo/r-package-devel), [RStudio community "package development" category](https://community.rstudio.com/c/package-development/11), [rOpenSci forum](https://discuss.ropensci.org/).

💡 Manage your subscriptions & involvement wisely!

---

# rOpenSci Software Peer Review

[Transparent, constructive, non adversarial and open review process](https://devguide.ropensci.org/softwarereviewintro.html#whatissoftwarereview) for packages [in scope](https://devguide.ropensci.org/policies.html#aims-and-scope).

Interesting for authors, and reviewers!

[Online book of best practice](https://devguide.ropensci.org/) for the reviews and package development.

🚀 Even more review and best practice on the way! [rOpenSci Statistical Software Peer Review](https://ropenscilabs.github.io/statistical-software-peer-review/)