class: center, middle, inverse, title-slide .title[ # Creating Packages in R ] .subtitle[ ## Focus: <em>Testing and Documentation</em> ] .author[ ### Colin E. Chisholm RPF, MSc ] .institute[ ### UNBC’s Aleza Lake Research Forest ] --- class: inverse center middle animated flipInY # Package Parts _Key package parts_ --- class: animate fadeIn background-image: url(./img/spare-parts-ChrisPo.jpg) background-size: 600px auto background-position:95% 55% ## Package Parts 1. Scripts 2. Testing 3. Data 4. Metadata 5. ... and more -- .small[_what about documentation?_] ??? 1. Scripts 2. Testing 3. Data 4. Metadata - DESCRIPTION - NAMESPACE - ... 5. ... and more --- class: middle background-image: url(./img/spare-parts-ChrisPo.jpg) background-size: 600px auto background-position:95% 55% .pull-left[ ## Packages for<br>Creating Packages ```r install.packages("devtools") install.packages("usethis") install.packages("testthat") install.packages("roxygen2") ``` ] --- class: inverse center middle animated flipInY # R Package Development ## A Workflow --- class: ## Workflow .pull-left[ 1. Initiate Package 2. Create Script 3. Test script ] .pull-right[ <ol start = "4"> <li>Auto-testing</li><br> <li>Documentation</li><br> <li>Add some data</li><br> </ol> ] -- .center[ _Once into the flow don't get too hung up on the order_ ] --- class:middle .pull-left[ ## Initiating a new package ] .pull-right[ _the `usethis` way_ ```r pithyname <- "/path/to/package" usethis::create_package(pithyname) usethis::use_git() ``` ] --- class: middle background-image: url(https://github.com/bcgov/bcgovr/raw/master/tools/readme/logo.png) background-size:100% auto; background-position:55% 33% ## Initiating a new package _the `bcgovr` way_ ```r remotes::install_github("bcgov/bcgovr") library(bcgovr) create_bcgov_project(path = "C:/my-new-project", coc_email = "my.email@gov.bc.ca") ``` .footnote[https://github.com/bcgov/bcgovr] --- .pull-left[ ## Create script ```r usethis::use_r("name_function") ``` .small[this creates `./R/name_function.R` and<br> by default opens it for editing] ] --- class: inverse middle center animated flipInY # Code it... _live coding_ --- ## Review: functions used ```r bcgovr::create_bcgov_package() usethis::use_r() devtools::load_all() ## CTRL + SHIFT + L ``` --- class: inverse middle center animated flipInY # Up next: `testthat` _live coding_ --- ## Review: functions used .pull-left[ ### First Steps ```r bcgovr::create_bcgov_package() usethis::use_r("function") devtools::load_all() ## CTRL + SHIFT + L ``` ] .pull-right[ ### Auto-testing ```r usethis::use_testthat() usethis::use_test("function") ``` ```r testthat::expect_equal() testthat::expect_error() devtools::test() ## CTRL + SHIFt + T ``` ```r covr::report() ``` ] --- ## Workflow .pull-left[ 1. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Initiated Package 2. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Created Script 3. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> ~~Tested~~ _Played_ with scripts ] .pull-right[ <ol start = "4"> <li><svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Auto-testing</li><br> <li>Documentation</li><br> <li>Add some data</li><br> </ol> ] --- class: inverse middle center animated flipInX # Documentation ## `roxygen2` --- class:middle .pull-left[  ## `roxygen2` `#'` to lead each line ] .pull-right[ <br> ### Essential tags - `@title` - `@description` - `@details` - `@params` - `@return` ] .footnote[https://roxygen2.r-lib.org] --- class: inverse middle center animated flipInY ## Code it --- ## Review: functions used .pull-left[ ```r bcgovr::create_bcgov_package() usethis::use_r("function") devtools::load_all() ## CTRL + SHIFT + L ``` ```r usethis::use_testthat() usethis::use_test("function") ``` ```r testthat::expect_equal() testthat::expect_error() devtools::test() ## CTRL + SHIFt + T ``` ] .pull-right[ Documentation ```r #' @title #' @description #' @details #' @param #' @return #' @examples devtools::document() ``` ] --- class: inverse middle center animated flipInY # Importing exisitng <br>scripts _Including the need for data_ --- background-image:url(img/aoi_snap.png) background-size: 400px; auto background-position: 95% 55% ## Example: `aoi_snap()` .left-column.small[ A script we have been using to ensure that various versions of the raster data can later stack. - _input_: an Area-of-Interest `sf` polygon - _output_: revised extent that is snapped to the closest 100m. ] --- ## Adding data .pull-left[ `usethis::use_data()` ] .pull-right[ <div id="htmlwidget-27d8a6c6199dca01cf8f" 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div.leaflet-popup-content {width:auto !important;overflow-y:auto; overflow-x:hidden;}<\/style><div style=\"max-height:25em;padding-right:0px;\"><table>\n\t\t\t <thead><tr><th colspan=\"2\"><b>L45514<\/b><\/th><\/thead><\/tr><tr><td style=\"color: #888888;\"><nobr>License<\/nobr><\/td><td align=\"right\"><nobr>L45514<\/nobr><\/td><\/tr><tr><td style=\"color: #888888;\"><nobr>Area<\/nobr><\/td><td align=\"right\"><nobr>9,002<\/nobr><\/td><\/tr><tr><td style=\"color: #888888;\"><nobr>Comment<\/nobr><\/td><td align=\"right\"><nobr>Aleza Lake Research Forest: Revised boundary from the 2001 original. Authorized by DPG-DM on Oct. 26, 2014<\/nobr><\/td><\/tr><\/table><\/div>",null,"L45514",{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]},{"method":"addLayersControl","args":[["Esri.WorldGrayCanvas","OpenStreetMap","Esri.WorldTopoMap"],["Esri.WorldTopoMap","dat"],{"collapsed":true,"autoZIndex":true,"position":"topleft"}]}],"limits":{"lat":[54.0041795,54.111254175591],"lng":[-122.1845757,-121.971719935868]},"fitBounds":[54.0041795,-122.1845757,54.111254175591,-121.971719935868,[]]},"evals":[],"jsHooks":[]}</script> ] --- class: inverse middle center animated flipInX # Code it _live coding_ --- ## Review: functions used .pull-left[ ```r bcgovr::create_bcgov_package() usethis::use_r("function") devtools::load_all() ## CTRL + SHIFT + L ``` ```r usethis::use_testthat() usethis::use_test("function") ``` ```r testthat::expect_equal() testthat::expect_error() devtools::test() ## CTRL + SHIFt + T ``` ] .pull-right[ ```r #' @title #' @description #' @details #' @param #' @return #' @examples devtools::document() ``` ```r usethis::use_data() ``` ] --- ## Workflow .pull-left[ 1. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Initiated Package 2. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Created Script 3. <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> ~~Tested~~ _Played_ with scripts ] .pull-right[ <ol start = "4"> <li><svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Auto-testing</li><br> <li><svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Documentation</li><br> <li><svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:green;height:1em;float:left;" xmlns="http://www.w3.org/2000/svg"> <path d="M256 8C119.033 8 8 119.033 8 256s111.033 248 248 248 248-111.033 248-248S392.967 8 256 8zm0 48c110.532 0 200 89.451 200 200 0 110.532-89.451 200-200 200-110.532 0-200-89.451-200-200 0-110.532 89.451-200 200-200m140.204 130.267l-22.536-22.718c-4.667-4.705-12.265-4.736-16.97-.068L215.346 303.697l-59.792-60.277c-4.667-4.705-12.265-4.736-16.97-.069l-22.719 22.536c-4.705 4.667-4.736 12.265-.068 16.971l90.781 91.516c4.667 4.705 12.265 4.736 16.97.068l172.589-171.204c4.704-4.668 4.734-12.266.067-16.971z"></path></svg> Add some data</li><br> </ol> ] --- class: animated flipInY background-image:url(https://r-pkgs.org/images/cover.png) background-position: 90% 50% background-size: 400px auto .pull-left[ # Resources - [R Packages (2e)](https://r-pkgs.org) - [Getting started with unit testing in R](https://www.pipinghotdata.com/posts/2021-11-23-getting-started-with-unit-testing-in-r/) - [`usethis`](https://usethis.r-lib.org) - [`testthat`](https://testthat.r-lib.org) - [`roxygen2`](https://roxygen2.r-lib.org) - [`bcgovr`](https://github.com/bcgov/bcgovr) ] --- class: inverse middle center animated flipInY # More ideas --- ## Name it ```r library(available) available("pemr") ``` .small[ ``` Name valid: ✔ Available on CRAN: ✔ Available on Bioconductor: ✔ Available on GitHub: ✖ Abbreviations: http://www.abbreviations.com/pem Wikipedia: https://en.wikipedia.org/wiki/pem Wiktionary: https://en.wiktionary.org/wiki/pem ```] --- ## `R` Code _don'ts_ 1. > Don’t use `library()` or `require()`.<br>.small[These modify the search path, affecting what functions are available from the global environment. Instead, you should use the `DESCRIPTION` to specify your package’s requirements ... This also makes sure those packages are installed when your package is installed.] 2. > Never use `source()` to load code from a file. .footnote[ https://r-pkgs.org/code.html#sec-code-load-all ] ??? Again the point of this is that you do not change the environment of the whoever is using the script. --- ## `R` Code _more don'ts_ .small[ > Here is a non-exhaustive list of other functions that should be used with caution: - [`options()`](https://rdrr.io/r/base/options.html) - [`par()`](https://rdrr.io/r/graphics/par.html) - [`setwd()`](https://rdrr.io/r/base/getwd.html) - [`Sys.setenv()`](https://rdrr.io/r/base/Sys.setenv.html) - [`Sys.setlocale()`](https://rdrr.io/r/base/locales.html) - [`set.seed()`](https://rdrr.io/r/base/Random.html) <br>.smaller[(or anything that changes the state of the random number generator)] ] .footnote[ https://r-pkgs.org/code.html#sec-code-load-all ] ??? Again the point of this is that you do not change the environment of the whoever is using the script.