Creating R packages

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.title[
# Creating R packages
]
.subtitle[
## Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology
]
.author[
### Andrea Sánchez-Tapia & Sara Mortara
]
.date[
### 9 Ago 2022
]

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### Why create R packages?

+ R philosophy: smooth transition from user to developer

+ Movement towards __diversifying the backgrounds of the developers__

+ Useful to share __sets of functions__ with a similar purpose, clean and usable __datasets__, __internal functions__ in labs or companies, or whole analyses

+ __Learning experience__ about portability, transparency, testing, contribution and collaboration

+ Knowing how packages are built allows you to __contribute__ to other people's packages

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## An R package

+ Has a special folder structure and files

+ Specific documentation for functions, datasets, vignettes, and additional articles
    
+ Needs a license

+ Can be built using tests

+ Submission to CRAN or keeping in GitHub

---
# File structure

```bash
.
├── .buildignore # Binary files and folders that won't be built
*├── DESCRIPTION  
*├── NAMESPACE    
*├── R/           # Functions
*├── man/         # Documentation
├── data/         # For data, called like: data(cars)
├── inst/         # Installation files
├── vignettes/   
└── README.md    
```

+ Some elements are mandatory (DESCRIPTION, NAMESPACE, R/, man/)
+ New project inside RStudio
+ Package __usethis__: `usethis::create_package()`

---
## Notes:

+ DESCRIPTION is edited by hand

+ Functions need to be documented inside each `.R` file, the rest of the files are created automatically by packages __devtools__ and __roxygen2__

+ Package __roxygen2__ will transform comments in `.R` into documentation inside `/man` and will fill the NAMESPACE, indicating which functions will be __imported__ or __exported__ by the package

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## During package development

+ The documentation is built using `devtools::document()`.

+ Check how the function populates the `/man` subfolder.

+ When your package is not installed but you want to check it, __load it__: `devtools::load_all()`

+ CRAN makes some automatic checks when you submit. Run these tests early and often, so you don't have trouble at the end: `devtools::check()`

+ A package can be installed directly from GitHub `remotes::install_github("profile/nameofthepackage")`

---

## More features

+ You can add tests for the functions with __testthat__

+ You can create a website for your package using __pkgdown__

+ Package __usethis__ automatizes lots of actions and creates the files needed to use __GitHub actions__

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