From 5675c8c72fcc126e572dfb79cb2aa3bec7482ffa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Florian=20Priv=C3=A9?= <florian.prive.21@gmail.com>
Date: Thu, 3 Oct 2024 06:42:51 +0200
Subject: [PATCH] update R-ladies slack link

---
 docs/404.html                                 |  6 ++++-
 docs/good-practices.html                      | 27 +++++++------------
 docs/good-practices.md                        | 16 +++++------
 .../gitbook-2.6.7/css/plugin-highlight.css    |  2 +-
 docs/search_index.json                        |  2 +-
 good-practices.Rmd                            |  2 +-
 6 files changed, 25 insertions(+), 30 deletions(-)

diff --git a/docs/404.html b/docs/404.html
index 7a8efa5..aaff386 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | Advanced R Course</title>
   <meta name="description" content="This contains materials for the Advanced R course of the doctoral school of Grenoble, France." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | Advanced R Course" />
   <meta property="og:type" content="book" />
@@ -129,6 +129,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="style.css" type="text/css" />
 </head>
diff --git a/docs/good-practices.html b/docs/good-practices.html
index 8b68c01..18b3a98 100644
--- a/docs/good-practices.html
+++ b/docs/good-practices.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Chapter 2 Good practices | Advanced R Course</title>
   <meta name="description" content="This contains materials for the Advanced R course of the doctoral school of Grenoble, France." />
-  <meta name="generator" content="bookdown 0.29 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Chapter 2 Good practices | Advanced R Course" />
   <meta property="og:type" content="book" />
@@ -129,6 +129,10 @@
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 </style>
 
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
 
 <link rel="stylesheet" href="style.css" type="text/css" />
 </head>
@@ -249,14 +253,15 @@
 <li class="chapter" data-level="6" data-path="packages.html"><a href="packages.html"><i class="fa fa-check"></i><b>6</b> Packages</a>
 <ul>
 <li class="chapter" data-level="6.1" data-path="packages.html"><a href="packages.html#resources"><i class="fa fa-check"></i><b>6.1</b> Resources</a></li>
-<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#project-exercise"><i class="fa fa-check"></i><b>6.2</b> Project exercise</a></li>
+<li class="chapter" data-level="6.2" data-path="packages.html"><a href="packages.html#package-exercise"><i class="fa fa-check"></i><b>6.2</b> Package exercise</a></li>
 <li class="chapter" data-level="6.3" data-path="packages.html"><a href="packages.html#pkg-start"><i class="fa fa-check"></i><b>6.3</b> Quick start</a></li>
-<li class="chapter" data-level="6.4" data-path="packages.html"><a href="packages.html#pkg-basics"><i class="fa fa-check"></i><b>6.4</b> Basic stuff</a>
+<li class="chapter" data-level="6.4" data-path="packages.html"><a href="packages.html#pkg-basics"><i class="fa fa-check"></i><b>6.4</b> Package basics</a>
 <ul>
 <li class="chapter" data-level="6.4.1" data-path="packages.html"><a href="packages.html#description-file"><i class="fa fa-check"></i><b>6.4.1</b> <em>DESCRIPTION</em> file</a></li>
 <li class="chapter" data-level="6.4.2" data-path="packages.html"><a href="packages.html#r-code"><i class="fa fa-check"></i><b>6.4.2</b> R code</a></li>
 <li class="chapter" data-level="6.4.3" data-path="packages.html"><a href="packages.html#documentation"><i class="fa fa-check"></i><b>6.4.3</b> Documentation</a></li>
 <li class="chapter" data-level="6.4.4" data-path="packages.html"><a href="packages.html#namespace-file"><i class="fa fa-check"></i><b>6.4.4</b> <em>NAMESPACE</em> file</a></li>
+<li class="chapter" data-level="6.4.5" data-path="packages.html"><a href="packages.html#exercise-2"><i class="fa fa-check"></i><b>6.4.5</b> Exercise</a></li>
 </ul></li>
 <li class="chapter" data-level="6.5" data-path="packages.html"><a href="packages.html#good-practices-1"><i class="fa fa-check"></i><b>6.5</b> Good practices</a>
 <ul>
@@ -577,7 +582,7 @@ <h3><span class="header-section-number">2.4.2</span> External help<a href="good-
 <p><img src="images/meme-SO.jpg" width="25%" style="display: block; margin: auto;" /></p>
 <p>You can ask questions on Stack Overflow (using the tag <code>r</code>). You need to <a href="https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example">make a great R reproducible example</a> if you want your question to be answered. Sometimes, while making this minimal reproducible example, you end up understanding and solving the issue on your own.</p>
 <p>If you are confident enough with your R skills, you can take the next step and <a href="https://stackoverflow.com/unanswered/tagged/r?tab=newest">answer questions on Stack Overflow</a>. It’s a good way to increase your skills, or just to <a href="https://privefl.github.io/blog/one-month-as-a-procrastinator-on-stack-overflow/">procrastinate while writing a scientific manuscript</a>.</p>
-<p>You can also join communities, e.g. <a href="https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM">join the French-speaking R community</a> or <a href="https://rladies-community-slack.herokuapp.com/">join the R-Ladies community</a> on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.</p>
+<p>You can also join communities, e.g. <a href="https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM">join the French-speaking R community</a> or <a href="https://airtable.com/appJZFYABfCIdPYMR/pagw7FJB5tm2UQ55o/form">join the R-Ladies community</a> on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.</p>
 
 </div>
 </div>
@@ -642,20 +647,6 @@ <h3><span class="header-section-number">2.4.2</span> External help<a href="good-
 });
 </script>
 
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-    if (location.protocol !== "file:")
-      if (/^https?:/.test(src))
-        src = src.replace(/^https?:/, '');
-    script.src = src;
-    document.getElementsByTagName("head")[0].appendChild(script);
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-</script>
 </body>
 
 </html>
diff --git a/docs/good-practices.md b/docs/good-practices.md
index 510bc1b..5ec641e 100644
--- a/docs/good-practices.md
+++ b/docs/good-practices.md
@@ -27,7 +27,7 @@ Most infix operators (`==`, `+`, `-`, `<-`, etc.) are also surrounded by
 spaces, except those with relatively high precedence: `^`, `:`, `::`, and `:::`. Always put a space after a comma, and never before (just like in regular English).
 
 
-```r
+``` r
 # Good
 average <- mean((feet / 12) + inches, na.rm = TRUE)
 x <- 1:10
@@ -44,7 +44,7 @@ base :: sum
 Curly braces, `{}`, define the most important hierarchy of R code. To make this hierarchy easy to see, always indent the code inside `{}` by two spaces. This should be automatic in RStudio.
 
 
-```r
+``` r
 # Good
 if (y < 0 && debug) {
   message("y is negative")
@@ -87,7 +87,7 @@ a separate function. In RStudio -> Tools -> Global Options, set
 - Use `<-`, not `=`, for assignment. Keep `=` for parameters.
 
 
-```r
+``` r
 # Good
 x <- 5
 system.time(
@@ -107,7 +107,7 @@ on the same line.
 - Only use `return()` for early returns. Otherwise rely on R to return the result of the last evaluated expression.
 
 
-```r
+``` r
 # Good
 add_two <- function(x, y) {
   x + y
@@ -122,7 +122,7 @@ add_two <- function(x, y) {
 - Use `"`, not `'`, for quoting text. The only exception is when the text already contains double quotes and no single quotes.
 
 
-```r
+``` r
 # Good
 "Text"
 'Text with "quotes"'
@@ -261,7 +261,7 @@ ssh-add <path_to_public_key>` (cf. [this SO answer](https://stackoverflow.com/a/
 A basic solution is to print everything, but it's usually not working well on complex problems. A convenient solution to see all the variables' states in your code is to place some `browser()` from where you want to check the variables' states. To debug functions, `debugonce()` is also very useful.
 
 
-```r
+``` r
 my_log <- function(x) log(x - 1)
 
 my_fun <- function(a, b) {
@@ -284,7 +284,7 @@ my_fun(1, 0)
 Try to uncomment `browser()` or use `debugonce(my_fun)`:
 
 
-```r
+``` r
 debugonce(my_fun)
 my_fun(1, 0)
 ```
@@ -306,4 +306,4 @@ You can ask questions on Stack Overflow (using the tag `r`). You need to [make a
 
 If you are confident enough with your R skills, you can take the next step and [answer questions on Stack Overflow](https://stackoverflow.com/unanswered/tagged/r?tab=newest). It's a good way to increase your skills, or just to [procrastinate while writing a scientific manuscript](https://privefl.github.io/blog/one-month-as-a-procrastinator-on-stack-overflow/).
 
-You can also join communities, e.g. [join the French-speaking R community](https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM) or [join the R-Ladies community](https://rladies-community-slack.herokuapp.com/) on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.
+You can also join communities, e.g. [join the French-speaking R community](https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM) or [join the R-Ladies community](https://airtable.com/appJZFYABfCIdPYMR/pagw7FJB5tm2UQ55o/form) on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.
diff --git a/docs/libs/gitbook-2.6.7/css/plugin-highlight.css b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
index 2aabd3d..02c0189 100644
--- a/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
+++ b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css
@@ -133,7 +133,7 @@
 .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code {
   /*
 
-Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
+Original Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
 
 */
   /* Solarized Green */
diff --git a/docs/search_index.json b/docs/search_index.json
index 466aece..28e7154 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
-[["packages.html", "Chapter 6 Packages 6.1 Resources 6.2 Package exercise 6.3 Quick start 6.4 Package basics 6.5 Good practices 6.6 More 6.7 Release on CRAN", " Chapter 6 Packages 6.1 Resources R Packages book (read it!) Writing R extensions, the official CRAN guide (easier to read as a bookdown) Look at popular R packages on GitHub Customizing Package Build Options Mastering Software Development in R How to develop good R packages (for open science) How to decide when to trust an R package? 6.2 Package exercise In my first package, I just put some functions I used again and again in my work. To experiment with making an R package, we’ll build a small package throughout this chapter. It will implement some of the features of package {dplyr} that we learned in chapter 4. We can call this package {minidplyr}. 6.3 Quick start To quickly start your package, just follow these steps: Create a new RStudio project (not a package). Here, I advise you to create a new project on GitHub (with a README) and then clone it as an RStudio project. It is a good practice to put all your (public) stuff on GitHub (as we learned in section 2.3). Run the following lines of R code. usethis::use_description(list(License = &quot;GPL-3&quot;)) usethis::use_namespace() dir.create(&quot;R&quot;) usethis::use_package_doc() usethis::use_roxygen_md() Restart RStudio and change the following options. You should see a new “Build” panel next to the “Git” panel. Then use Ctrl/Cmd + Shift + B to build and reload your package. Create a simple function and put it in an .R file in the R/ directory. Inside the function, use Code -&gt; Insert Roxygen Skeleton. Build and reload your package and check the documentation of your new function and that you can use it. 6.4 Package basics 6.4.1 DESCRIPTION file See this chapter on the DESCRIPTION file. 6.4.2 R code Put your R code in the R/ directory. Basically it would be mostly functions. Don’t use random lines of code like in R scripts. Never explicitly load a package with library() or require(). Use usethis::use_package() to add one package to your DESCRIPTION file. Then, refer to some function with &lt;package&gt;::&lt;function&gt;() in your code, or by using the @import &lt;package&gt; or @importFrom &lt;package&gt; &lt;function&gt; roxygen tags. If one R function need another function in another R file, use the @import &lt;basename&gt;.R to make sure it is built and documented before; it is for example useful if you define new generics and methods in different files. If you modify global options() or graphics par() in a function of your package (try to avoid it), save the old values and reset when you are done: old &lt;- options(stringsAsFactors = FALSE) on.exit(options(old), add = TRUE) 6.4.3 Documentation Documentation is super useful for other people (including future-you, in 6 months when you won’t remember what you implemented in your package). Make sure to document your code as soon as you write it, otherwise you will never do it. Forget about the man/ (manual) directory, files in this directory will be automatically generated thanks to the roxygen comments you use on top of your R functions. Learn more with this chapter. Note that you can now use the Markdown syntax in the documentation. For example, instead of having to use \\code{foo}, you can directly use `foo` in the roxygen comments. To use (and export) functions already implemented in other packages, for example the pipe from package {magrittr}, you can use usethis::use_package(\"magrittr\") and put the following code somewhere in an R file of your package. #&#39; @importFrom magrittr %&gt;% #&#39; @export magrittr::`%&gt;%` Fun: [How to] Include a dancing banana in your R package documentation. 6.4.4 NAMESPACE file You can also forget about this for now because it should be automatically generated by {roxygen}. If you want to understand what’s going on, read this chapter. 6.4.5 Exercise Create a first function that helps you select variables of a data frame by using a character vector of variable names or an integer vector of variable positions. Which accessor could you use? Document this function and use it. Check your package with Ctrl/Cmd + Shift + E and fix all problems. At this point, there should be no ERROR or WARNING, unless you did not document the previous function properly. However, you should still update the DESCRIPTION file with proper information. Do it, fix any problem, and run checks again. You could almost submit this package to CRAN in its current form; congratulations on your new R package! Commit everything and push to GitHub. Try to install the package from someone else using remotes::install_github(\"&lt;github-username&gt;/minidplyr\"). 6.5 Good practices 6.5.1 Testing You are probably already testing your code, you’re only doing it informally. The problem with this approach is that when you come back to this code in 3 months time to add a new feature, you’ve probably forgotten some of the informal tests you ran the first time around. This makes it very easy to break existing code that used to work (which you should avoid as much as you can). A very good practice is to use unit tests. Read this chapter. To make your first unit tests, use usethis::use_test() while having open the R file you want to test. Write some unit tests, then you can run tests of your package with Ctrl/Cmd + Shift + T. Add unit tests for your new function select2. Which silly cases you should test? Here you can use usethis::use_package(\"dplyr\", type = \"Suggests\") to add package {dplyr} to the suggested packages (because you will use this package in tests only). You can see the unit tests I came up with for this function. Make a function filter2 that enables to filter rows of a data frame. Add some documentation and tests for this function as well. 6.5.2 Continuous checking I would rarely trust a package that doesn’t use these continuous integration services. It’s good practice to check your package regularly and on different Operating Systems (OS). Learn more about the different checks there. An easy way to regularly check your package on GitHub is to use GitHub Actions. Indeed, each time you push to your GitHub repository, checks are run on different OS. To use this service, you can run usethis::use_github_action(\"check-standard\"). To get the coverage of your tests, use Codecov by running usethis::use_coverage() and usethis::use_github_action(\"test-coverage\"). Finally, to prevent typos in your package and especially for non-native English speakers, it can be useful to check the spelling in your package. If you think that the word “programmation” exists and that “prefered” has only one ‘r’ at the end (I did!), you should definitely use package {spelling}. Just run spelling::spell_check_setup(); this will check spelling in your package at the end of checks. If it reports words you want to ignore, just put these words in a text file inst/WORDLIST (with one word per line). Set this up. Check your package locally, then commit and push your changes. Go check your new badges on GitHub! 6.5.3 Pkgdown Run usethis::use_pkgdown(). If added, remove docs from the .gitignore file. Run pkgdown:::build_site(). On GitHub, go to the settings of your repo, and enable GitHub Pages from the /docs folder. Push the new files. This will render everything that you have in this folder as a website (after 0-2 minutes). You will find your package’s website at https://&lt;github-username&gt;.github.io/minidplyr/. To get more information and especially to configure the website, see the documentation, as a {pkgdown} website, of course. For an example, see the website of my package {bigstatsr} and the corresponding YAML file. If you want to make a personal website, check this quick tutorial. 6.6 More 6.6.1 Rcpp We learned about Rcpp in section 5.4. To use Rcpp code in your package, just run usethis::use_rcpp(). Then, create .cpp files with RStudio and save them the src/ directory. Note that the // [[Rcpp::export]] makes the C++ function available to R, it doesn’t export the function as part of your package (though you could access it with &lt;package&gt;:::&lt;rcpp-fun&gt;()). If you want your package to explicitly provides an Rcpp function (as an R function), you also need roxygen comments (beginning with //' instead of #', including //' @export) on top of your Rcpp function. If you need some C++ code from another package (e.g. from package {RcppArmadillo}), normally you would use // [[Rcpp::depends(RcppArmadillo)]] #include &lt;RcppArmadillo.h&gt; In an R package, you don’t need the first line // [[Rcpp::depends(RcppArmadillo)]], but instead you need to add the package to the LinkingTo field of the DESCRIPTION file (e.g. with usethis::use_package(\"RcppArmadillo\", \"LinkingTo\")). 6.6.2 Ignore files There are two types of ignore: Files ignored by Git, specified in the .gitignore file. For example, you don’t want to track changes for some large data files or some binaries often changing. You can ignore files by using usethis::use_git_ignore(). Files ignored during the build of your package, specified in the .Rbuildignore file. For example, in my packages, I generally have directories called tmp-tests and tmp-data where I put code and data that I used during development, but that should not be part of the final package. Checks will tell you if your package contains non-standard files or directories. Moreover, I generally ignore vignettes; they are still built as part of the {pkgdown} website. There is also a {usethis} function for this: usethis::use_build_ignore(). 6.6.3 The inst/ directory When a package is installed, everything in inst/ is copied into the top-level package directory. For example, you can have: inst/extdata/: additional external data for examples and vignettes. See section 6.6.4 for more detail. You can also use inst/testdata/ for data you need in tests. To access one file in this directory, use system.file(). For example, if you have a file inst/extdata/mydata.csv in your package, an user can find it using system.file(\"extdata\", \"mydata.csv\", package = \"&lt;package&gt;\"). inst/include: some C++ code that others can use by LinkingTo your package. For example, when you use #include &lt;Rcpp.h&gt; at the top of your Rcpp code, you’re using the code in there. inst/CITATION: how to cite the package. Learn more there. 6.6.4 External data Learn more with this book chapter. 6.7 Release on CRAN If you want your package to be on CRAN, read this chapter. "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
+[["good-practices.html", "Chapter 2 Good practices 2.1 Coding style 2.2 RStudio 2.3 Version control (Git) 2.4 Getting help", " Chapter 2 Good practices 2.1 Coding style Good coding style is like correct punctuation: you can manage without it, butitsuremakesthingseasiertoread. – Hadley Wickham Please make your code readable by following e.g. this coding style. Hereinafter I provide some examples from this guide. You can use package styler (that provides RStudio addins) to correct your style: You can also use Ctrl+Shift+A in RStudio; we will talk about RStudio shortcuts in section 2.2. 2.1.1 Naming Be smart with your naming. I can’t tell the number of times I’ve seen df &lt;- as.matrix(mtcars) on Stack Overflow. 2.1.2 Spacing Put a space before and after = when naming arguments in function calls. Most infix operators (==, +, -, &lt;-, etc.) are also surrounded by spaces, except those with relatively high precedence: ^, :, ::, and :::. Always put a space after a comma, and never before (just like in regular English). # Good average &lt;- mean((feet / 12) + inches, na.rm = TRUE) x &lt;- 1:10 base::sum # Bad average&lt;-mean(feet/12+inches,na.rm=TRUE) x &lt;- 1 : 10 base :: sum 2.1.3 Indenting Curly braces, {}, define the most important hierarchy of R code. To make this hierarchy easy to see, always indent the code inside {} by two spaces. This should be automatic in RStudio. # Good if (y &lt; 0 &amp;&amp; debug) { message(&quot;y is negative&quot;) } if (y == 0) { if (x &gt; 0) { log(x) } else { message(&quot;x is negative or zero&quot;) } } else { y ^ x } # Bad if (y &lt; 0 &amp;&amp; debug) message(&quot;Y is negative&quot;) if (y == 0) { if (x &gt; 0) { log(x) } else { message(&quot;x is negative or zero&quot;) } } else { y ^ x } 2.1.4 Long lines Strive to limit your code to 80 characters per line. This fits comfortably on your screen with a reasonably sized font. If you find yourself running out of room, this is a good indication that you should encapsulate some of the work in a separate function. In RStudio -&gt; Tools -&gt; Global Options, set 2.1.5 Other Use &lt;-, not =, for assignment. Keep = for parameters. # Good x &lt;- 5 system.time( x &lt;- rnorm(1e6) ) # Bad x = 5 system.time( x = rnorm(1e6) ) Don’t put ; at the end of a line, and avoid multiple commands on the same line. Only use return() for early returns. Otherwise rely on R to return the result of the last evaluated expression. # Good add_two &lt;- function(x, y) { x + y } # Bad add_two &lt;- function(x, y) { return(x + y) } Use \", not ', for quoting text. The only exception is when the text already contains double quotes and no single quotes. # Good &quot;Text&quot; &#39;Text with &quot;quotes&quot;&#39; &#39;&lt;a href=&quot;http://style.tidyverse.org&quot;&gt;A link&lt;/a&gt;&#39; # Bad &#39;Text&#39; &#39;Text with &quot;double&quot; and \\&#39;single\\&#39; quotes&#39; 2.2 RStudio Download a recent enough version of RStudio (&gt;= 1.2) and use it! Learn more about the new features of RStudio at https://rstudio.com/products/rstudio/release-notes/. RStudio features: everything you can expect from a good IDE keyboard shortcuts I use Ctrl + Space (auto-completion, better than Tab) Ctrl + Up (command history &amp; search) Ctrl + Click (function source code) Ctrl + Enter (execute line of code) Ctrl + Shift + A (reformat code) Ctrl + Shift + C (comment/uncomment selected lines) Ctrl + Shift + K (knit) Ctrl + Shift + B (build package, website or book) Ctrl + Shift + M (pipe) Alt + Shift + K to see all shortcuts… Panels (everything is integrated, including Git and a terminal) Interactive data importation from files and connections (see this webinar) Use code diagnostics: RStudio Projects: Meaningful structure in one folder The working directory automatically switches to the project’s folder The File tab displays the associated files and folders in the project History of R commands and open files Any settings associated with the project, such as Git settings, are loaded. Note that you can have a .Rprofile file in the project’s root directory to enable project-specific settings to be loaded each time people open the project. Read more at https://www.tidyverse.org/articles/2017/12/workflow-vs-script/ and also see chapter Efficient set-up of book Efficient R programming. 2.3 Version control (Git) 2.3.1 Why use Git? You don’t use Git? Figure 2.1: You don’t use Version Control? Have you ever: Made a change to code, realized it was a mistake and wanted to revert back? Lost code or had a backup that was too old? Wanted to submit a change to someone else’s code? Wanted to share your code, or let other people work on your code? In these cases, and probably many others, a version control system should make your life easier (see https://stackoverflow.com/a/1408464/6103040). Version control for the researcher: don’t do that, use Git Version control for the data analyst: reproducible workflow Also, see https://stackoverflow.com/q/2712421/6103040. Use version control to work from anywhere Working with GitHub can be a line on your CV (read more): A lot of students have said to me later, even first-year undergraduates, that using GitHub has helped them a lot when they went for an internship or a research position interview. They are able to say, “Oh, I already have worked with GitHub. I am familiar with it. I know how it works.” So I think they are at least able to put that on their CV and go into a situation where there’s a research or data analysis team and say, “Yeah, sure. I am actually familiar with the same tools that you use.” – Mine Cetinkaya-Rundel, Duke University, RStudio Be able to get websites for your packages with pkgdown, for your book (like this one!) with bookdown, for your personal webpage with R Markdown Websites or blogdown. 2.3.2 About Git Main Git platforms (share your code, collaborate): GitHub, documentation (only free for public repositories, now owned by Microsoft) GitLab (open source &amp; free) Bitbucket (free when you have less than 5 collaborators) any server.. 4 main commands: add: add files to be part of the next commit commit: snapshot of your code at a specified point in time (you can and you should use this even when having no internet connection) push: merge your local modifications with the main project pull: update your local project with the latest version of the main project Simple (solo) use of git to prevent merge conflicts: after opening a project, always pull before closing a project, always commit/push Use git even when you do not have any internet connection! (e.g. on a secure server) Just use commits for version control locally. How to link between an RStudio project and a GitHub repository? For Mac users, you might need to use the terminal for git clone, then create the RStudio project from the existing directory. If you have some permission denied for the public key, you might also need to run ssh-agent -s &amp;&amp; ssh-add &lt;path_to_public_key&gt; (cf. this SO answer). Help with Git: Happy Git and GitHub for the useR Git cheat sheet When things go wrong To fix a mistake Create a new branch with git and manage branches 2.4 Getting help 2.4.1 Help yourself, learn how to debug A basic solution is to print everything, but it’s usually not working well on complex problems. A convenient solution to see all the variables’ states in your code is to place some browser() from where you want to check the variables’ states. To debug functions, debugonce() is also very useful. my_log &lt;- function(x) log(x - 1) my_fun &lt;- function(a, b) { # browser() la &lt;- my_log(a) lb &lt;- my_log(b) la + lb } my_fun(1, 0) #&gt; Warning in log(x - 1): NaNs produced #&gt; [1] NaN Try to uncomment browser() or use debugonce(my_fun): debugonce(my_fun) my_fun(1, 0) Learn more with this book chapter, this other book chapter, this webinar and this RStudio article. 2.4.2 External help Can’t remember useful functions? Use cheat sheets. You can search for specific R stuff on https://rseek.org/. You should also read documentations carefully. If you’re using a package, search for vignettes and a GitHub repository. You can also use Stack Overflow. The most common use of Stack Overflow is when you have an error or a question, you google it, and most of the times the first links are Q/A on Stack Overflow. You can ask questions on Stack Overflow (using the tag r). You need to make a great R reproducible example if you want your question to be answered. Sometimes, while making this minimal reproducible example, you end up understanding and solving the issue on your own. If you are confident enough with your R skills, you can take the next step and answer questions on Stack Overflow. It’s a good way to increase your skills, or just to procrastinate while writing a scientific manuscript. You can also join communities, e.g. join the French-speaking R community or join the R-Ladies community on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow. "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
diff --git a/good-practices.Rmd b/good-practices.Rmd
index 139e2ac..cccb8ab 100644
--- a/good-practices.Rmd
+++ b/good-practices.Rmd
@@ -308,4 +308,4 @@ You can ask questions on Stack Overflow (using the tag `r`). You need to [make a
 
 If you are confident enough with your R skills, you can take the next step and [answer questions on Stack Overflow](https://stackoverflow.com/unanswered/tagged/r?tab=newest). It's a good way to increase your skills, or just to [procrastinate while writing a scientific manuscript](https://privefl.github.io/blog/one-month-as-a-procrastinator-on-stack-overflow/).
 
-You can also join communities, e.g. [join the French-speaking R community](https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM) or [join the R-Ladies community](https://rladies-community-slack.herokuapp.com/) on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.
+You can also join communities, e.g. [join the French-speaking R community](https://join.slack.com/t/r-grrr/shared_invite/enQtMzI4MzgwNTc4OTAxLWZlOGZiZTBiMWU0NDQ3OTYzOGE1YThiODgwZWNhNWEyYjI4ZDJiNmNhY2YyYWI5YzFiOTFkNDYxYzkwODUwNWM) or [join the R-Ladies community](https://airtable.com/appJZFYABfCIdPYMR/pagw7FJB5tm2UQ55o/form) on Slack. These are generally much friendlier and welcoming spaces compared to Stack Overflow.