diff --git a/404.html b/404.html
index 4e665db..b2779f2 100644
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="https://frbcesab.github.io/rcompendium/index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index da9780e..9b2c6ac 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
index ce8d9cc..a3d8783 100644
--- a/CONTRIBUTING.html
+++ b/CONTRIBUTING.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 68511b8..e1c3ec5 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png
index c9b49e6..e17234e 100644
Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ
diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png
index f5c41f1..fe9f799 100644
Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ
diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png
index 47aa16a..6d50ca4 100644
Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ
diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png
index fed74c8..8185b44 100644
Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ
diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png
index e482f65..83cd45a 100644
Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ
diff --git a/apple-touch-icon.png b/apple-touch-icon.png
index c606a04..e1aa4f0 100644
Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ
diff --git a/articles/developing_a_package.html b/articles/developing_a_package.html
index eb7706a..1035c6a 100644
--- a/articles/developing_a_package.html
+++ b/articles/developing_a_package.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 5e191a6..36167b2 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/rcompendium.html b/articles/rcompendium.html
index 86eda7c..6ce372e 100644
--- a/articles/rcompendium.html
+++ b/articles/rcompendium.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/working_with_a_compendium.html b/articles/working_with_a_compendium.html
index ea44258..352f44f 100644
--- a/articles/working_with_a_compendium.html
+++ b/articles/working_with_a_compendium.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 54acdcc..0c27012 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/favicon-16x16.png b/favicon-16x16.png
index 6486868..117ea3c 100644
Binary files a/favicon-16x16.png and b/favicon-16x16.png differ
diff --git a/favicon-32x32.png b/favicon-32x32.png
index 195dc20..c6cc168 100644
Binary files a/favicon-32x32.png and b/favicon-32x32.png differ
diff --git a/index.html b/index.html
index 4b5ac59..1c7d968 100644
--- a/index.html
+++ b/index.html
@@ -51,7 +51,7 @@
     
     <a class="navbar-brand me-2" href="index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 7522964..9b4a50f 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -54,6 +54,9 @@
       <small>Source: <a href="https://github.com/FRBCesab/rcompendium/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.3.9000" id="rcompendium-139000-development-version">rcompendium 1.3.9000 (development version)<a class="anchor" aria-label="anchor" href="#rcompendium-139000-development-version"></a></h2>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.3" id="rcompendium-13">rcompendium 1.3<a class="anchor" aria-label="anchor" href="#rcompendium-13"></a></h2><p class="text-muted">CRAN release: 2023-10-26</p>
 <ul><li>
diff --git a/pkgdown.yml b/pkgdown.yml
index c3d1adb..953c013 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   developing_a_package: developing_a_package.html
   rcompendium: rcompendium.html
   working_with_a_compendium: working_with_a_compendium.html
-last_built: 2024-01-23T13:58Z
+last_built: 2024-01-23T14:19Z
 urls:
   reference: https://frbcesab.github.io/rcompendium/reference
   article: https://frbcesab.github.io/rcompendium/articles
diff --git a/reference/add_citation.html b/reference/add_citation.html
index 4db1a70..59382d7 100644
--- a/reference/add_citation.html
+++ b/reference/add_citation.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_code_of_conduct.html b/reference/add_code_of_conduct.html
index 362ae5c..fa7d158 100644
--- a/reference/add_code_of_conduct.html
+++ b/reference/add_code_of_conduct.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_codecov_badge.html b/reference/add_codecov_badge.html
index 8e9570e..02bc91b 100644
--- a/reference/add_codecov_badge.html
+++ b/reference/add_codecov_badge.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_compendium.html b/reference/add_compendium.html
index bce9fd4..d27208a 100644
--- a/reference/add_compendium.html
+++ b/reference/add_compendium.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_contributing.html b/reference/add_contributing.html
index b5d963b..d268c3b 100644
--- a/reference/add_contributing.html
+++ b/reference/add_contributing.html
@@ -32,7 +32,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_cran_badge.html b/reference/add_cran_badge.html
index 983aa28..e142903 100644
--- a/reference/add_cran_badge.html
+++ b/reference/add_cran_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_dependencies.html b/reference/add_dependencies.html
index bffbaba..b502315 100644
--- a/reference/add_dependencies.html
+++ b/reference/add_dependencies.html
@@ -50,7 +50,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_dependencies_badge.html b/reference/add_dependencies_badge.html
index 53b7fc4..f751f52 100644
--- a/reference/add_dependencies_badge.html
+++ b/reference/add_dependencies_badge.html
@@ -28,7 +28,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_description.html b/reference/add_description.html
index 8072cf2..24e88d0 100644
--- a/reference/add_description.html
+++ b/reference/add_description.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_dockerfile.html b/reference/add_dockerfile.html
index 9854959..d5741cf 100644
--- a/reference/add_dockerfile.html
+++ b/reference/add_dockerfile.html
@@ -46,7 +46,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_check.html b/reference/add_github_actions_check.html
index 45345f8..c460c29 100644
--- a/reference/add_github_actions_check.html
+++ b/reference/add_github_actions_check.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_check_badge.html b/reference/add_github_actions_check_badge.html
index 1e0cdec..9b21d49 100644
--- a/reference/add_github_actions_check_badge.html
+++ b/reference/add_github_actions_check_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_citation.html b/reference/add_github_actions_citation.html
index 7880c96..e10fbd7 100644
--- a/reference/add_github_actions_citation.html
+++ b/reference/add_github_actions_citation.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_codecov.html b/reference/add_github_actions_codecov.html
index 3dccb1d..ee1f5d1 100644
--- a/reference/add_github_actions_codecov.html
+++ b/reference/add_github_actions_codecov.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_codecov_badge.html b/reference/add_github_actions_codecov_badge.html
index a6bb82c..946fc95 100644
--- a/reference/add_github_actions_codecov_badge.html
+++ b/reference/add_github_actions_codecov_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_document.html b/reference/add_github_actions_document.html
index ccf8286..5c10a78 100644
--- a/reference/add_github_actions_document.html
+++ b/reference/add_github_actions_document.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_pkgdown.html b/reference/add_github_actions_pkgdown.html
index 02cf9a9..e5cc5b9 100644
--- a/reference/add_github_actions_pkgdown.html
+++ b/reference/add_github_actions_pkgdown.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_pkgdown_badge.html b/reference/add_github_actions_pkgdown_badge.html
index 27cfedf..451e8d0 100644
--- a/reference/add_github_actions_pkgdown_badge.html
+++ b/reference/add_github_actions_pkgdown_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_github_actions_render.html b/reference/add_github_actions_render.html
index 6ba5218..f8e686e 100644
--- a/reference/add_github_actions_render.html
+++ b/reference/add_github_actions_render.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_license.html b/reference/add_license.html
index b48b738..e9a6404 100644
--- a/reference/add_license.html
+++ b/reference/add_license.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_license_badge.html b/reference/add_license_badge.html
index 3dd46e8..6b925bf 100644
--- a/reference/add_license_badge.html
+++ b/reference/add_license_badge.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_lifecycle_badge.html b/reference/add_lifecycle_badge.html
index 7a18e37..527c404 100644
--- a/reference/add_lifecycle_badge.html
+++ b/reference/add_lifecycle_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_makefile.html b/reference/add_makefile.html
index 3dc12ed..1d3ff27 100644
--- a/reference/add_makefile.html
+++ b/reference/add_makefile.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_package_doc.html b/reference/add_package_doc.html
index d40cccf..895a44d 100644
--- a/reference/add_package_doc.html
+++ b/reference/add_package_doc.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_r_depend.html b/reference/add_r_depend.html
index 6f372e1..cc9f713 100644
--- a/reference/add_r_depend.html
+++ b/reference/add_r_depend.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_readme_rmd.html b/reference/add_readme_rmd.html
index 3eab717..d99e2d4 100644
--- a/reference/add_readme_rmd.html
+++ b/reference/add_readme_rmd.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_renv.html b/reference/add_renv.html
index 8ec180a..7ff120e 100644
--- a/reference/add_renv.html
+++ b/reference/add_renv.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_repostatus_badge.html b/reference/add_repostatus_badge.html
index 8326596..6cba5d8 100644
--- a/reference/add_repostatus_badge.html
+++ b/reference/add_repostatus_badge.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_testthat.html b/reference/add_testthat.html
index c956710..82da9d8 100644
--- a/reference/add_testthat.html
+++ b/reference/add_testthat.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_to_buildignore.html b/reference/add_to_buildignore.html
index ac32bfa..d45b2b6 100644
--- a/reference/add_to_buildignore.html
+++ b/reference/add_to_buildignore.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_to_gitignore.html b/reference/add_to_gitignore.html
index 0a13b91..ca268c2 100644
--- a/reference/add_to_gitignore.html
+++ b/reference/add_to_gitignore.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_vignette.html b/reference/add_vignette.html
index 407ce0f..5f73db2 100644
--- a/reference/add_vignette.html
+++ b/reference/add_vignette.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_all_dependencies.html b/reference/get_all_dependencies.html
index 5d4dd92..b90b906 100644
--- a/reference/get_all_dependencies.html
+++ b/reference/get_all_dependencies.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_all_functions.html b/reference/get_all_functions.html
index 5d85a6c..eecc99e 100644
--- a/reference/get_all_functions.html
+++ b/reference/get_all_functions.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_licenses.html b/reference/get_licenses.html
index 0ac13ad..4900000 100644
--- a/reference/get_licenses.html
+++ b/reference/get_licenses.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_minimal_r_version.html b/reference/get_minimal_r_version.html
index ce3d205..77f570e 100644
--- a/reference/get_minimal_r_version.html
+++ b/reference/get_minimal_r_version.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index e690840..9b82582 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -66,7 +66,7 @@ <h2 id="prerequisites">Prerequisites<a class="anchor" aria-label="anchor" href="
 
       <dl><dt>
           
-          <code><a href="rcompendium-package.html">rcompendium-package</a></code> <code><a href="rcompendium-package.html">_PACKAGE</a></code> <code><a href="rcompendium-package.html">rcompendium</a></code> 
+          <code><a href="rcompendium-package.html">rcompendium-package</a></code> <code><a href="rcompendium-package.html">rcompendium</a></code> 
         </dt>
         <dd>Create a package or research compendium structure</dd>
       </dl></div><div class="section level2">
diff --git a/reference/new_compendium.html b/reference/new_compendium.html
index ee3545d..a63a6d9 100644
--- a/reference/new_compendium.html
+++ b/reference/new_compendium.html
@@ -72,7 +72,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/new_package.html b/reference/new_package.html
index 24ebbc9..6e23d2e 100644
--- a/reference/new_package.html
+++ b/reference/new_package.html
@@ -60,7 +60,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rcompendium-package.html b/reference/rcompendium-package.html
index ddc0eed..cda8b1a 100644
--- a/reference/rcompendium-package.html
+++ b/reference/rcompendium-package.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/refresh.html b/reference/refresh.html
index 1b9de97..0fe0df2 100644
--- a/reference/refresh.html
+++ b/reference/refresh.html
@@ -30,7 +30,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/set_credentials.html b/reference/set_credentials.html
index f804161..c15d258 100644
--- a/reference/set_credentials.html
+++ b/reference/set_credentials.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">rcompendium</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.3.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 8dd35cf..ae5b371 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement nicolas.casajus@fondationbiodiversite.fr. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to rcompendium","title":"Contributing to rcompendium","text":"First , thanks taking time contribute rcompendium! types contributions encouraged valued. See Table contents different ways help details project handles . Please make sure read relevant section making contribution. make lot easier us maintainers smooth experience involved.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contributing to rcompendium","text":"Code conduct Style guide Commit messages Asking questions Reporting bugs Requesting features Contributing code","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of conduct","title":"Contributing to rcompendium","text":"project released Contributor Code Conduct. participating, expected uphold code. Please report unacceptable behavior nicolas.casajus@fondationbiodiversite.fr.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"","what":"Style guide","title":"Contributing to rcompendium","text":"use Tidyverse style guide writing R code. Functions documented roxygen2 syntax. rcompendium uses lower_snake_case.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"commit-messages","dir":"","previous_headings":"","what":"Commit messages","title":"Contributing to rcompendium","text":"want contribute commiting changes, please try use Conventional commits specification.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"asking-questions","dir":"","previous_headings":"","what":"Asking questions","title":"Contributing to rcompendium","text":"ask question, best search existing Issues might help . case found suitable issue still need clarification, can write question issue. still feel need ask question need clarification, recommend following: Open new Issue. Use template other_issue.md. Provide much context can ’re running . Provide project platform versions (paste output sessionInfo()). take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"before-submitting-a-bug-report","dir":"","previous_headings":"Reporting bugs","what":"Before submitting a bug report","title":"Contributing to rcompendium","text":"good bug report shouldn’t leave others needing chase information. Therefore, ask investigate carefully, collect information describe issue detail report. Please complete following steps advance help us fix potential bug fast possible. Make sure using latest version rcompendium. Determine bug really bug error side. see users experienced (potentially already solved) issue , check already bug report existing bug error bug tracker.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"how-do-i-submit-a-bug-report","dir":"","previous_headings":"Reporting bugs","what":"How do I submit a bug report?","title":"Contributing to rcompendium","text":"use GitHub Issues track bugs errors. run issue project: Open new Issue. Use template bug_report.md. Explain behavior expect actual behavior. Please provide much context possible describe reproduction steps someone else can follow recreate issue . usually includes code reproducible example. take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"before-requesting-a-feature","dir":"","previous_headings":"Requesting features","what":"Before requesting a feature","title":"Contributing to rcompendium","text":"Make sure using latest version rcompendium. Read documentation carefully find functionality already covered. Perform search see enhancement already suggested. , add comment existing issue instead opening new one.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"how-do-i-submit-a-feature-request","dir":"","previous_headings":"Requesting features","what":"How do I submit a feature request?","title":"Contributing to rcompendium","text":"Feature requests tracked GitHub Issues. Open new Issue. Use template feature_request.md. Provide clear descriptive title issue identify suggestion. Provide step--step description suggested enhancement many details possible. Explain enhancement useful rcompendium users. take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"general-workflow","dir":"","previous_headings":"Contributing code","what":"General workflow","title":"Contributing to rcompendium","text":"use GitHub flow collaborate project: Fork repository using GitHub interface. Clone fork using git clone fork-url (replace fork-url URL fork). Alternatively, open RStudio IDE create New Project Version Control. Create new branch w/ git checkout -b branch-name (replace branch-name name new branch). Make contribution (see examples). Stage (git add) commit (git commit) changes often necessary Push changes GitHub w/ git push origin branch-name. Submit Pull Request original repo. review PR soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-the-readme","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing the README","title":"Contributing to rcompendium","text":"want contribute improving README, please edit README.Rmd (README.md). forget update README.md running:","code":"rmarkdown::render(\"README.Rmd\")"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-vignettes","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing vignettes","title":"Contributing to rcompendium","text":"want contribute editing existing vignette, just edit corresponding Rmd file stored vignettes/ folder. want contribute adding new vignette, create new Rmd file vignettes/ folder add following header: use new external dependency, forget add DESCRIPTION file section Suggests (package already listed section Imports). Check integrity package :","code":"--- title: \"Vignette Title\" output: rmarkdown::html_vignette vignette: >   %\\VignetteIndexEntry{Vignette Title}   %\\VignetteEngine{knitr::rmarkdown}   %\\VignetteEncoding{UTF-8} --- devtools::check()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-function-documentation","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing function documentation","title":"Contributing to rcompendium","text":"want contribute improving documentation function, open corresponding file R/ folder edit lines starting #' (roxygen2 syntax). Update documentation (Rd files man/ folder) running: use new external dependency example section, forget add DESCRIPTION file section Imports (package already listed). Check integrity package :","code":"devtools::document() devtools::check()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"fix-bug","dir":"","previous_headings":"Contributing code","what":"Fix bug","title":"Contributing to rcompendium","text":"want contribute improving code function, open edit corresponding file R/ folder. Check integrity package : forget adapt unit tests function editing corresponding file stored tests/testthat/ folder. use package testthat implement unit tests. Check tests running:","code":"devtools::check() devtools::test()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"new-feature","dir":"","previous_headings":"Contributing code","what":"New feature","title":"Contributing to rcompendium","text":"want contribute submitting new feature, please follow workflow: Create new R file folder R/. Implement code function. Document function w/ roxygen2 syntax. necessary, add additional dependencies DESCRIPTION file. Update package documentation w/ devtools::document(). Create new R file folder tests/testthat/. Implement unit tests new function. Check integrity package w/ devtools::check(). Thanks contribution!","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 2, June 1991Copyright © 1989, 1991 Free Software Foundation, Inc.,51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"licenses software designed take away freedom share change . contrast, GNU General Public License intended guarantee freedom share change free software–make sure software free users. General Public License applies Free Software Foundation’s software program whose authors commit using . (Free Software Foundation software covered GNU Lesser General Public License instead.) can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge service wish), receive source code can get want , can change software use pieces new free programs; know can things. protect rights, need make restrictions forbid anyone deny rights ask surrender rights. restrictions translate certain responsibilities distribute copies software, modify . example, distribute copies program, whether gratis fee, must give recipients rights . must make sure , , receive can get source code. must show terms know rights. protect rights two steps: (1) copyright software, (2) offer license gives legal permission copy, distribute /modify software. Also, author’s protection , want make certain everyone understands warranty free software. software modified someone else passed , want recipients know original, problems introduced others reflect original authors’ reputations. Finally, free program threatened constantly software patents. wish avoid danger redistributors free program individually obtain patent licenses, effect making program proprietary. prevent , made clear patent must licensed everyone’s free use licensed . precise terms conditions copying, distribution modification follow.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"terms-and-conditions-for-copying-distribution-and-modification","dir":"","previous_headings":"","what":"TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION","title":"GNU General Public License","text":"0. License applies program work contains notice placed copyright holder saying may distributed terms General Public License. “Program”, , refers program work, “work based Program” means either Program derivative work copyright law: say, work containing Program portion , either verbatim modifications /translated another language. (Hereinafter, translation included without limitation term “modification”.) licensee addressed “”. Activities copying, distribution modification covered License; outside scope. act running Program restricted, output Program covered contents constitute work based Program (independent made running Program). Whether true depends Program . 1. may copy distribute verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice disclaimer warranty; keep intact notices refer License absence warranty; give recipients Program copy License along Program. may charge fee physical act transferring copy, may option offer warranty protection exchange fee. 2. may modify copy copies Program portion , thus forming work based Program, copy distribute modifications work terms Section 1 , provided also meet conditions: ) must cause modified files carry prominent notices stating changed files date change. b) must cause work distribute publish, whole part contains derived Program part thereof, licensed whole charge third parties terms License. c) modified program normally reads commands interactively run, must cause , started running interactive use ordinary way, print display announcement including appropriate copyright notice notice warranty (else, saying provide warranty) users may redistribute program conditions, telling user view copy License. (Exception: Program interactive normally print announcement, work based Program required print announcement.) requirements apply modified work whole. identifiable sections work derived Program, can reasonably considered independent separate works , License, terms, apply sections distribute separate works. distribute sections part whole work based Program, distribution whole must terms License, whose permissions licensees extend entire whole, thus every part regardless wrote . Thus, intent section claim rights contest rights work written entirely ; rather, intent exercise right control distribution derivative collective works based Program. addition, mere aggregation another work based Program Program (work based Program) volume storage distribution medium bring work scope License. 3. may copy distribute Program (work based , Section 2) object code executable form terms Sections 1 2 provided also one following: ) Accompany complete corresponding machine-readable source code, must distributed terms Sections 1 2 medium customarily used software interchange; , b) Accompany written offer, valid least three years, give third party, charge cost physically performing source distribution, complete machine-readable copy corresponding source code, distributed terms Sections 1 2 medium customarily used software interchange; , c) Accompany information received offer distribute corresponding source code. (alternative allowed noncommercial distribution received program object code executable form offer, accord Subsection b .) source code work means preferred form work making modifications . executable work, complete source code means source code modules contains, plus associated interface definition files, plus scripts used control compilation installation executable. However, special exception, source code distributed need include anything normally distributed (either source binary form) major components (compiler, kernel, ) operating system executable runs, unless component accompanies executable. distribution executable object code made offering access copy designated place, offering equivalent access copy source code place counts distribution source code, even though third parties compelled copy source along object code. 4. may copy, modify, sublicense, distribute Program except expressly provided License. attempt otherwise copy, modify, sublicense distribute Program void, automatically terminate rights License. However, parties received copies, rights, License licenses terminated long parties remain full compliance. 5. required accept License, since signed . However, nothing else grants permission modify distribute Program derivative works. actions prohibited law accept License. Therefore, modifying distributing Program (work based Program), indicate acceptance License , terms conditions copying, distributing modifying Program works based . 6. time redistribute Program (work based Program), recipient automatically receives license original licensor copy, distribute modify Program subject terms conditions. may impose restrictions recipients’ exercise rights granted herein. responsible enforcing compliance third parties License. 7. , consequence court judgment allegation patent infringement reason (limited patent issues), conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. distribute satisfy simultaneously obligations License pertinent obligations, consequence may distribute Program . example, patent license permit royalty-free redistribution Program receive copies directly indirectly , way satisfy License refrain entirely distribution Program. portion section held invalid unenforceable particular circumstance, balance section intended apply section whole intended apply circumstances. purpose section induce infringe patents property right claims contest validity claims; section sole purpose protecting integrity free software distribution system, implemented public license practices. Many people made generous contributions wide range software distributed system reliance consistent application system; author/donor decide willing distribute software system licensee impose choice. section intended make thoroughly clear believed consequence rest License. 8. distribution /use Program restricted certain countries either patents copyrighted interfaces, original copyright holder places Program License may add explicit geographical distribution limitation excluding countries, distribution permitted among countries thus excluded. case, License incorporates limitation written body License. 9. Free Software Foundation may publish revised /new versions General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies version number License applies “later version”, option following terms conditions either version later version published Free Software Foundation. Program specify version number License, may choose version ever published Free Software Foundation. 10. wish incorporate parts Program free programs whose distribution conditions different, write author ask permission. software copyrighted Free Software Foundation, write Free Software Foundation; sometimes make exceptions . decision guided two goals preserving free status derivatives free software promoting sharing reuse software generally.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"no-warranty","dir":"","previous_headings":"","what":"NO WARRANTY","title":"GNU General Public License","text":"11. PROGRAM LICENSED FREE CHARGE, WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION. 12. EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MAY MODIFY /REDISTRIBUTE PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES. END TERMS CONDITIONS","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively convey exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program interactive, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, commands use may called something show w show c; even mouse-clicks menu items–whatever suits program. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. sample; alter names: General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker.  <signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice"},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"package-content","dir":"Articles","previous_headings":"","what":"Package content","title":"Developing an R package","text":"First, create new empty RStudio project. Let’s called pkg. create new package structure, run rcompendium::new_package(). default, following content created:  addition, new GitHub repository created directly R. available : https://github.com/{{account}}/pkg/ ({{account}} either GitHub account GitHub organization). minutes later, website (pkgdown) deployed : https://{{account}}.github.io/pkg/.","code":"pkg/                              # Root of the package │ ├── pkg.Rproj                     # RStudio project (created by user, optional) │ ├── .git/                         # GIT tracking folder ├── .gitignore                    # List of files/folders to be ignored by GIT |                                 # (specific to R language) | ├── .github/                      # (optional) GitHub Actions settings │   └── workflows/ │       ├── pkgdown.yaml          # Configuration file to build & deploy website │       ├── R-CMD-check.yaml      # Configuration file to check & test package │       ├── render-README.yaml    # Configuration file to render the README.md │       └── test-coverage.yaml    # Configuration file to report code coverage │ ├── _pkgdown.yaml                 # (optional) User website settings │ ├── R/                            # R functions location │   ├── fun-demo.R                # Example of an R function (to remove) │   └── pkg-package.R             # Dummy R file for package-level documentation │ ├── man/                          # R functions helps (automatically updated) │   ├── print_msg.Rd              # Documentation of the demo R function │   ├── pkg-package.Rd            # Package-level documentation │   └── figures/                  # Figures for the README  │       └── package-sticker.png   # Package sticker template │ ├── tests/                        # (optional) Units tests location │   ├── testthat.R                # Units tests settings │   └── testthat/                 # Units tests location │       └── test-demo.R           # Units tests for the demo function (to remove) | ├── vignettes/                    # (optional) Vignettes location │   └── pkg.Rmd                   # Get started tutorial                          [*] │ ├── DESCRIPTION                   # Project metadata                              [*] ├── LICENSE.md                    # Content of the GPL (>= 2) license (default) ├── NAMESPACE                     # Automatically generated ├── .Rbuildignore                 # List of files/folders to be ignored while  │                                 # checking/installing the package ├── inst/ │   ├── CITATION                  # BiBTeX entry to cite the package              [*] │   └── package-sticker/ │       ├── package-sticker.R     # Code to generate package sticker │       └── r_logo.png            # R logo │ ├── README.md                     # GitHub README (automatically generated) └── README.Rmd                    # GitHub README                                 [*]   [*] These files are automatically created but user needs to manually add      some information."},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"description","dir":"Articles","previous_headings":"Package metadata","what":"DESCRIPTION","title":"Developing an R package","text":"DESCRIPTION file contains important package metadata. default, rcompendium creates following file: information, please read https://r-pkgs.org/description.html. N.B. change Title, Description, Version, Authors@R values, forget also change citation information inst/CITATION README.Rmd.","code":"Package: pkg Type: Package Title: The Title of the Project                                              [*] Version: 0.0.0.9000 Authors@R: c(     person(given   = \"John\",            family  = \"Doe\",            role    = c(\"aut\", \"cre\", \"cph\"),            email   = \"john.doe@domain.com\",            comment = c(ORCID = \"9999-9999-9999-9999\"))) Description: A paragraph providing a full description of the project (on     [*]      several lines...) URL: https://github.com/jdoe/pkg BugReports: https://github.com/jdoe/pkg/issues License: GPL (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 VignetteBuilder: knitr Suggests:      knitr,     rmarkdown,     testthat (>= 3.0.0) Config/testthat/edition: 3   [*] Title and Description must be adapted by user."},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"readme","dir":"Articles","previous_headings":"Package metadata","what":"README","title":"Developing an R package","text":"README.md homepage repository GitHub. purpose help visitor understand project. Always edit README.Rmd (.md version). information, please read https://r-pkgs.org/release.html#readme.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"recommended-workflow","dir":"Articles","previous_headings":"","what":"Recommended workflow","title":"Developing an R package","text":"recommended workflow : Implement new function R/ Document function using roxygen syntax Update functions doc (man/) NAMESPACE devtools::document() Update list required packages DESCRIPTION rcompendium::add_dependencies() Implement units tests using testthat Edit vignette illustrate new feature Check test package devtools::check() can also provide data package. See ?usethis::use_data.  strongly recommend read book R packages Hadley Wickham Jenny Bryan.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"resources","dir":"Articles","previous_headings":"","what":"Resources","title":"Developing an R package","text":"R packages Hadley Wickham Jenny Bryan Writing R extensions R Development Core Team Extending R John M. Chambers","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"prerequisites","dir":"Articles","previous_headings":"","what":"Prerequisites","title":"Get started with rcompendium","text":"using package rcompendium must follow three steps.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"git-configuration","dir":"Articles","previous_headings":"Prerequisites","what":"GIT configuration","title":"Get started with rcompendium","text":"First ensure GIT correctly installed machine linked RStudio. Read Chapter 6 Happy Git GitHub useR. also need store GIT credentials locally (.e. project) globally (recommended). Run gh::gh_whoami() see git associated credentials correctly configured. see something like: Otherwise might need run: See ?gert::git_config_global_set information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name = \"user.name\",   value = \"John Doe\") gert::git_config_global_set(name = \"user.email\",  value = \"john.doe@domain.com\") gert::git_config_global_set(name = \"github.user\", value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"creating-a-github-repo","dir":"Articles","previous_headings":"Prerequisites","what":"Creating a GitHub repo","title":"Get started with rcompendium","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). don’t GITHUB PAT locally stored, must: visit page https://github.com/settings/tokens create new token; store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9'. Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured, see something like calling gh::gh_whoami(): able create GitHub repository directly R!","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"delete_repo, repo, workflow\",   \"token\": \"ghp_99z9...z9\" }"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"managing-credentials","dir":"Articles","previous_headings":"Prerequisites","what":"Managing credentials","title":"Get started with rcompendium","text":"can use arguments given, family, email, orcid directly functions new_*() add_*(). create lot projects (packages /compendia) can frustrating long run. alternative way use function set_credentials() permanently store information ~/.Rprofile file. arguments set NULL calling function package, rcompendium search values file. save time (’s purpose package). Even stored credentials ~/.Rprofile file always able modify --fly (.e. using credentials arguments functions new_*() add_*()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"usage","dir":"Articles","previous_headings":"","what":"Usage","title":"Get started with rcompendium","text":"recommended workflow : Store credentials set_credentials() (already done); IMPORTANT - Create new empty RStudio project; Run new_package() create new package structure new_compendium() create new research compendium structure; Edit metadata DESCRIPTION, CITATION, README.Rmd; Start working (add data, write document R functions, etc.); forget commit changes.  addition three setup functions (set_credentials(), new_package(), new_compendium()), package rcompendium offers 29 functions. can grouped : add_*(): functions add/update/overwrite files, configuration settings, dependencies, badges, etc.; get_*(): functions retrieve information (available licenses, R version, etc.). Visit Reference page details.  sum N.B. Users can also use functions package usethis add missing features (e.g. data/ package release tools).","code":"## Define ONCE FOR ALL your credentials ----  rcompendium::set_credentials(given = \"John\", family = \"Doe\",                               email = \"john.doe@domain.com\",                               orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")   ## CREATE A NEW EMPTY RSTUDIO PROJECT ----   ## Create an R package structure ----  rcompendium::new_package()   ## Then...  ## ... edit metadata in DESCRIPTION, CITATION, README.Rmd, etc. ## ... implement and document R functions in R/   ## Update functions documentation and NAMESPACE ----  devtools::document()   ## Update list of dependencies in DESCRIPTION ----  rcompendium::add_dependencies()   ## Check package ----  devtools::check()   ## Example: use of an add_*() function ... ## ... update 'Number of Dependencies Badge' in README.Rmd ----  rcompendium::add_dependencies_badge()"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"resources","dir":"Articles","previous_headings":"","what":"Resources","title":"Get started with rcompendium","text":"Developing R package Working compendium","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"contributing","dir":"Articles","previous_headings":"","what":"Contributing","title":"Get started with rcompendium","text":"welcome contribute rcompendium project. Please read Contribution Guidelines. Please note rcompendium project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"colophon","dir":"Articles","previous_headings":"","what":"Colophon","title":"Get started with rcompendium","text":"package result intense discussions feedback training course Data Toolbox Reproducible Research Computational Ecology. rcompendium largely inspired package rrtools developed Ben Marwick et al. tries respect standard defined community. Special thanks developers!","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"compendium-content","dir":"Articles","previous_headings":"","what":"Compendium content","title":"Working with a Compendium","text":"First, create new empty RStudio project. Let’s called comp. create new compendium structure, run rcompendium::new_compendium(). default, following content created:  create_repo = TRUE (default), new GitHub repository created directly R. available : https://github.com/{{account}}/comp/ ({{account}} either GitHub account GitHub organization). repository can private private = TRUE.","code":"comp/                             # Root of the compendium │ ├── comp.Rproj                    # RStudio project (created by user, optional) │ ├── .git/                         # GIT tracking folder ├── .gitignore                    # List of files/folders to be ignored by GIT |                                 # (specific to R language) │ ├── R/                            # R functions location │   ├── fun-demo.R                # Example of an R function (to remove) │   └── comp-package.R            # Dummy R file for high-level documentation │ ├── man/                          # R functions helps (automatically updated) │   ├── print_msg.Rd              # Documentation of the demo R function │   └── pkg-package.Rd            # High-level documentation │ ├── DESCRIPTION                   # Project metadata                              [*] ├── LICENSE.md                    # Content of the GPL (>= 2) license (default) ├── NAMESPACE                     # Automatically generated ├── .Rbuildignore                 # List of files/folders to be ignored while  │                                 # checking/installing the package │ ├── README.md                     # GitHub README (automatically generated) ├── README.Rmd                    # GitHub README                                 [*] │ ├── data/                         # User raw data (.csv, .gpkg, etc.) │   ├── raw-data/                 # Read-only files │   └── derived-data/             # Modified data derived from raw data │ ├── analyses/                     # R scripts (not function) to run analyses │ ├── outputs/                      # Outputs (R objects, .csv, etc.) ├── figures/                      # Figures (.png, .pdf, etc.) │ └── make.R                        # Main R script to source all R scripts                                    # stored in analyses/  [*] These files are automatically created but user needs to manually add      some information."},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"description","dir":"Articles","previous_headings":"Compendium metadata","what":"DESCRIPTION","title":"Working with a Compendium","text":"DESCRIPTION file contains important compendium metadata. default rcompendium creates following file: DESCRIPTION file specific R package can used work research compendia (see ). information edit file, please read https://r-pkgs.org/description.html.","code":"Package: comp Type: Package Title: The Title of the Project                                              [*] Version: 0.0.0.9000 Authors@R: c(     person(given   = \"John\",            family  = \"Doe\",            role    = c(\"aut\", \"cre\", \"cph\"),            email   = \"john.doe@domain.com\",            comment = c(ORCID = \"9999-9999-9999-9999\"))) Description: A paragraph providing a full description of the project (on     [*]      several lines...) URL: https://github.com/jdoe/comp BugReports: https://github.com/jdoe/comp/issues License: GPL (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 Imports:      devtools,     here  [*] Title and Description must be adapted by user."},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"readme","dir":"Articles","previous_headings":"Compendium metadata","what":"README","title":"Working with a Compendium","text":"README.md homepage repository GitHub. purpose help visitor understand project. Always edit README.Rmd (.md version). information, please read https://r-pkgs.org/release.html?q=README#readme.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"recommendations","dir":"Articles","previous_headings":"","what":"Recommendations","title":"Working with a Compendium","text":"Keep root project clean possible Store raw data data/raw-data/ Document raw data modifications (R scripts /R functions) Export modified raw data data/derived-data/ (outputs/) Store R functions R/ Store R scripts /Rmd analyses/ Control project make.R file (add lines source R scripts) Built relative paths using ::() Call external functions package::function() Alternatively add #' @import package (#' @importFrom package function) R/comp-package.R call external functions function() Use devtools::document() update NAMESPACE Use rcompendium::add_dependencies(\".\") update list required dependencies DESCRIPTION use install.packages() remotes::install_deps() (install required dependencies listed DESCRIPTION) use library() devtools::load_all() (load required dependencies listed DESCRIPTION R functions stored R/) source functions use instead devtools::load_all() document everything!","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"using-renv","dir":"Articles","previous_headings":"Advanced features","what":"Using renv","title":"Working with a Compendium","text":"default structure created rcompendium::new_compendium() good starting point making analyses reproducible. can increase reproducibility using package renv. renv freeze exact package versions depend (renv.lock). ensures collaborator (future) use exact versions packages. Moreover renv provides project private package library making project isolated others. initialize renv compendium, use renv = TRUE rcompendium::new_compendium() call function rcompendium::add_renv() rcompendium::new_compendium(). make.R also updated (replacement remotes::install_deps() renv::restore())  Working renv Work usual Update NAMESPACE devtools::document() Update required dependencies DESCRIPTION rcompendium::add_dependencies(\".\") Install required dependencies locally renv::install() Save local environment renv::snapshot()","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"using-docker","dir":"Articles","previous_headings":"Advanced features","what":"Using docker","title":"Working with a Compendium","text":"Docker tool creates self-contained environment (containers) within operating system, system libraries software (.e. R, RStudio server) frozen ready--use. use container requires recipe (Dockerfile) describes steps needed create environment. recipe, Docker image built: template container created. information Docker R users: https://environments.rstudio.com/docker add Dockerfile compendium, use dockerfile = TRUE rcompendium::new_compendium() call function rcompendium::add_dockerfile() rcompendium::new_compendium(). default rcompendium creates following Dockerfile:  use renv Docker (recommended) last step look like:  default Docker image based rocker/rstudio. can customize Dockerfile (e.g. adding system dependencies) use different default Docker image (.e. tidyverse, verse, geospatial, etc.). information: https://github.com/rocker-org/rocker-versioned2 versions R renv (applicable) specified Dockerfile local system. image built, whole project added image. container launched default working directory root project.  project ready shared, collaborator () must follow steps: Clone repository Build Docker image (terminal) Dockerfile running: docker build -t \"image_name\" . (can take time) Start container (terminal) new Docker image image_name running: docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true image_name Open Web browser visit 127.0.0.1:8787: new instance RStudio Server available everything ready--use (data, code, packages, etc.) reproduce analysis, run: source(\"make.R\")","code":"FROM rocker/rstudio:4.1.3  MAINTAINER John Doe <john.doe@domain.com>   ## Install system dependencies (for devtools) ----  RUN sudo apt update -yq \\  && sudo apt install --no-install-recommends libxml2-dev -yq \\  && sudo apt clean all \\  && sudo apt purge \\  && sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*   ## Copy local project ----  ENV folder=\"/home/rstudio/\"  COPY . $folder RUN chown -R rstudio:rstudio $folder   ## Set working directory ----  WORKDIR $folder   ## Install R packages ----  RUN R -e \"install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))\" \\  && R -e \"remotes::install_deps(upgrade = 'never')\" ## Install R packages ----  ENV RENV_VERSION 0.15.4  RUN R -e \"install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))\" \\  && R -e \"remotes::install_github('rstudio/renv@${RENV_VERSION}')\" \\  && sudo -u rstudio R -e \"renv::restore()\""},{"path":"https://frbcesab.github.io/rcompendium/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nicolas Casajus. Author, maintainer, copyright holder.","code":""},{"path":"https://frbcesab.github.io/rcompendium/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Casajus N. (2023). rcompendium: R package create package research compendium structure. R package version 1.3, https://github.com/FRBCesab/rcompendium.","code":"@Manual{,   title = {{rcompendium}: {An} {R} package to create a package or research compendium structure},   author = {{Casajus N.}},   year = {2023},   note = {R package version 1.3},   url = {https://github.com/FRBCesab/rcompendium}, }"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"rcompendium-","dir":"","previous_headings":"","what":"Create a Package or Research Compendium Structure","title":"Create a Package or Research Compendium Structure","text":"area open science, making reproducible analyses strong prerequisite. sometimes difficult 1) find good structure organize files 2) set whole project. aim package rcompendium make easier creation R package/research compendium (.e. predefined files/folders structure) users can focus code/analysis instead wasting time organizing files. full ready--work structure set following features: Initialization version control git. Creation minimal R package structure (DESCRIPTION NAMESPACE files, R/ man/ folders). Creation additional files (LICENSE.md, inst/CITATION, etc.). Creation Get started vignette vignettes/ (package ). Setting units tests process tests/. Creation README.Rmd HexSticker (template) badges. Autocompletion maintainer information. Initialization renv system (required). Creation Dockerfile (required). Creation GitHub repository. check test package (R CMD Check); report code coverage (covr); build deploy website (pkgdown); render README.md. package heavily relies R packages devtools usethis follows recommendations made Hadley Wickham & Jenny Bryan Ben Marwick.","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create a Package or Research Compendium Structure","text":"can install stable version CRAN : can install development version GitHub : Note: Unix system may error installation linked V8 JavaScript engine. software required R package cffr (included rcompendium). Run following line try reinstall rcompendium.","code":"## Install stable version of < rcompendium > from CRAN ---- install.packages(\"rcompendium\") ## Install < remotes > package (if not already installed) ---- if (!requireNamespace(\"remotes\", quietly = TRUE)) {   install.packages(\"remotes\") }  ## Install dev version of < rcompendium > from GitHub ---- remotes::install_github(\"FRBCesab/rcompendium\") ## Fix V8 issues ---- Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)  ## Install < rcompendium > ---- install.packages(\"rcompendium\")"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create a Package or Research Compendium Structure","text":"Please read Get started vignette pay attention sections Prerequisites Usage Others available vignettes: Developing Package Working Compendium","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Create a Package or Research Compendium Structure","text":"Please cite package : Casajus N. (2023) rcompendium: R package create package research compendium structure. Version 1.3, https://github.com/FRBCesab/rcompendium. can also run:","code":"citation(\"rcompendium\")  ## A BibTeX entry for LaTeX users is: ##  ## @Manual{, ##   title  = {{rcompendium}: {An} {R} package to create a package or research compendium structure}, ##   author = {{Casajus N.}}, ##   year   = {2023}, ##   note   = {R package version 1.3}, ##   url    = {https://github.com/FRBCesab/rcompendium}, ## }"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Create a Package or Research Compendium Structure","text":"types contributions encouraged valued. information, check Contribution Guidelines. Please note rcompendium project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"colophon","dir":"","previous_headings":"","what":"Colophon","title":"Create a Package or Research Compendium Structure","text":"package result intense discussions feedbacks training course Reproducible Research Computational Ecology. rcompendium largely inspired package rrtools developed Ben Marwick et al. tries respect standard defined community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a CITATION file — add_citation","title":"Create a CITATION file — add_citation","text":"function creates CITATION file folder inst/. file contains BiBTeX entry cite package manual. User need edit hand information (title, version, etc.).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a CITATION file — add_citation","text":"","code":"add_citation(   given = NULL,   family = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a CITATION file — add_citation","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a CITATION file — add_citation","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a CITATION file — add_citation","text":"","code":"if (FALSE) { add_citation() readCitationFile(\"inst/CITATION\") citation(\"pkg\")    # If you have installed your package <pkg> }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":null,"dir":"Reference","previous_headings":"","what":"Add code of conduct — add_code_of_conduct","title":"Add code of conduct — add_code_of_conduct","text":"function creates CODE_OF_CONDUCT.md file adapted Contributor Covenant, version 2.1 available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add code of conduct — add_code_of_conduct","text":"","code":"add_code_of_conduct(   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add code of conduct — add_code_of_conduct","text":"email character length 1. email address project maintainer. open logical value. TRUE (default) CONTRIBUTING.md file opened editor. overwrite logical value. files already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add code of conduct — add_code_of_conduct","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add code of conduct — add_code_of_conduct","text":"","code":"if (FALSE) { add_code_of_conduct() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Codecov badge — add_codecov_badge","title":"Add a Codecov badge — add_codecov_badge","text":"function adds Code coverage badge README.Rmd, .e. percentage code cover units tests. percentage computed codecov.io service. Note: service must manually activated package visiting https://.codecov.io/. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Codecov badge — add_codecov_badge","text":"","code":"add_codecov_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Codecov badge — add_codecov_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Codecov badge — add_codecov_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Codecov badge — add_codecov_badge","text":"","code":"if (FALSE) { add_codecov_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":null,"dir":"Reference","previous_headings":"","what":"Create additional folders — add_compendium","title":"Create additional folders — add_compendium","text":"function creates compendium, .e. additional folders package structure. default, following directories created: data/raw-data, data/derived-data, analyses/, outputs/, figures/. README.md added folder must edited. argument compendium allows user choose compendium structure. theses folders added .Rbuildignore file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create additional folders — add_compendium","text":"","code":"add_compendium(compendium = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create additional folders — add_compendium","text":"compendium character vector specifying folders created. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create additional folders — add_compendium","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create additional folders — add_compendium","text":"","code":"if (FALSE) { add_compendium() add_compendium(compendium = \"paper\") add_compendium(compendium = c(\"data\", \"outputs\", \"code\", \"manuscript\")) }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":null,"dir":"Reference","previous_headings":"","what":"Add contribution guidelines — add_contributing","title":"Add contribution guidelines — add_contributing","text":"function creates several files help user learn contribute project: CONTRIBUTING.md: general guidelines outlining best way contribute project (can modified); .github/ISSUE_TEMPLATE/bug_report.md: issue template report bug (can modified); .github/ISSUE_TEMPLATE/feature_request.md: issue template suggest new feature (can modified); .github/ISSUE_TEMPLATE/other_issue.md: issue template types issue (can modified).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add contribution guidelines — add_contributing","text":"","code":"add_contributing(   email = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add contribution guidelines — add_contributing","text":"email character length 1. email address project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) CONTRIBUTING.md file opened editor. overwrite logical value. files already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add contribution guidelines — add_contributing","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add contribution guidelines — add_contributing","text":"","code":"if (FALSE) { add_contributing() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a CRAN Status badge — add_cran_badge","title":"Add a CRAN Status badge — add_cran_badge","text":"function adds CRAN Status badge README.Rmd. package hosted CRAN badge indicate published CRAN. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a CRAN Status badge — add_cran_badge","text":"","code":"add_cran_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a CRAN Status badge — add_cran_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a CRAN Status badge — add_cran_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a CRAN Status badge — add_cran_badge","text":"","code":"if (FALSE) { add_cran_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Add dependencies in DESCRIPTION — add_dependencies","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"function detects external dependencies used R/, NAMESPACE, @examples sections roxygen2 headers automatically adds dependencies Imports section DESCRIPTION file. NAMESPACE function detects dependencies mentioned import(pkg) importFrom(pkg,fun). R/ folder detects functions called pkg::fun() code R files. @examples sections also detects packages attached library() require(). vignettes/ folder also inspected detected dependencies (pkg::fun(), library() require()) added Suggests field DESCRIPTION file (addition packages knitr rmarkdown). project research compendium user can also inspect additional folder(s) argument compendium add dependencies Imports section DESCRIPTION file. detection process one used vignettes/. tests/ folder also inspected detected dependencies (pkg::fun(), library() require()) added Suggests field DESCRIPTION file (addition package testthat).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"","code":"add_dependencies(compendium = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"compendium character length 1. name folder recursively detect dependencies added Imports field DESCRIPTION file. can 'analysis/' (additional folders, .e. data/, outputs/, figures/, etc. created folder), '.' (folders data/, outputs/, figures/, etc. created root project), etc. See new_compendium() information. Default compendium = NULL (.e. additional folder inspected R/, NAMESPACE, vignettes/, tests/ still inspected).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"","code":"if (FALSE) { add_dependencies() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Dependencies badge — add_dependencies_badge","title":"Add a Dependencies badge — add_dependencies_badge","text":"function adds updates Dependencies badge README.Rmd. first number corresponds direct dependencies second recursive dependencies. Note: function can work packages published CRAN based function gtools::getDependencies(). See also function get_all_dependencies(). Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Dependencies badge — add_dependencies_badge","text":"","code":"add_dependencies_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Dependencies badge — add_dependencies_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Dependencies badge — add_dependencies_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Dependencies badge — add_dependencies_badge","text":"","code":"if (FALSE) { add_dependencies_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a DESCRIPTION file — add_description","title":"Create a DESCRIPTION file — add_description","text":"function creates DESCRIPTION file root project. file contains metadata project. information (title, description, version, etc.) must edited hand. information: https://r-pkgs.org/description.html. User credentials can passed arguments recommended store .Rprofile file set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a DESCRIPTION file — add_description","text":"","code":"add_description(   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a DESCRIPTION file — add_description","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. orcid character length 1. ORCID project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. open logical value. TRUE (default) file opened editor. overwrite logical value. DESCRIPTION already present overwrite = TRUE, file erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a DESCRIPTION file — add_description","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a DESCRIPTION file — add_description","text":"","code":"if (FALSE) { add_description(organisation = \"MySociety\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Dockerfile — add_dockerfile","title":"Create a Dockerfile — add_dockerfile","text":"function creates Dockerfile root project based template. Docker image based rocker/rstudio. whole project copied image R packages installed (using renv::restore() remotes::install_deps()). addition .dockerignore file added ignore files/folders building image. User can customize Dockerfile (e.g. system dependencies). /can also use different default Docker image (.e. tidyverse, verse, geospatial, etc.). information: https://github.com/rocker-org/rocker-versioned2 default versions R renv (applicable) specified Dockerfile local system. project ready released, user must build Docker image running: docker build -t \"image_name\" . run container, user must run: docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true image_name new instance RStudio Server available Web browser URL: 127.0.0.1:8787.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Dockerfile — add_dockerfile","text":"","code":"add_dockerfile(   given = NULL,   family = NULL,   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Dockerfile — add_dockerfile","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. open logical value. TRUE (default) Dockerfile opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Dockerfile — add_dockerfile","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a Dockerfile — add_dockerfile","text":"","code":"if (FALSE) { add_dockerfile() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to check package — add_github_actions_check","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"function creates configuration file (.yaml) setup GitHub Actions check package. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/R-CMD-check.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"","code":"add_github_actions_check(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"return value.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"workflow runs R CMD check three major operating systems (Ubuntu, macOS, Windows) using latest release R. package also checked Ubuntu (latest version) using development previous versions R.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"","code":"if (FALSE) { add_github_actions_check() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a R CMD Check badge — add_github_actions_check_badge","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"function adds R CMD Check badge README.Rmd. function must run add_github_actions_check() setup GitHub Actions check test package. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"","code":"add_github_actions_check_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"","code":"if (FALSE) { add_github_actions_check_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"function creates configuration file (.yaml) setup GitHub Actions update CITATION.cff. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/update-citation-cff.yaml. function also create CITATION.cff using package cffr.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"","code":"add_github_actions_citation(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"","code":"if (FALSE) { add_github_actions_citation() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"function creates configuration file (.yaml) setup GitHub Actions report code coverage testing package. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/test-coverage.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"","code":"add_github_actions_codecov(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"","code":"if (FALSE) { add_github_actions_codecov() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Test coverage badge — add_github_actions_codecov_badge","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"function adds Test coverage badge README.Rmd. function must run add_github_actions_codecov() setup GitHub Actions report percentage code cover units tests. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"","code":"add_github_actions_codecov_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"","code":"if (FALSE) { add_github_actions_codecov_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to document package — add_github_actions_document","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"function creates configuration file (.yaml) setup GitHub Actions document package update Rd files man/, NAMESPACE DESCRIPTION files. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/document-package.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"","code":"add_github_actions_document(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"","code":"if (FALSE) { add_github_actions_document() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"function creates configuration file (.yaml) setup GitHub Actions automatically build deploy website using pkgdown. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/pkgdown.yaml. additional empty file (_pkgdown.yaml) also written: can used customize website.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"","code":"add_github_actions_pkgdown(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"","code":"if (FALSE) { add_github_actions_pkgdown() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Website badge — add_github_actions_pkgdown_badge","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"function adds Website badge README.Rmd. function must run add_github_actions_pkgdown() setup GitHub Actions build deploy package website. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"","code":"add_github_actions_pkgdown_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"","code":"if (FALSE) { add_github_actions_pkgdown_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to render README — add_github_actions_render","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"function creates configuration file (.yaml) setup GitHub Actions automatically knit README.Rmd push. workflow triggered README.Rmd modified since last commit. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/render-README.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"","code":"add_github_actions_render(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"","code":"if (FALSE) { add_github_actions_render() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a LICENSE — add_license","title":"Add a LICENSE — add_license","text":"function adds license project. add license name License field DESCRIPTION file write content license License.md file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a LICENSE — add_license","text":"","code":"add_license(license = NULL, given = NULL, family = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a LICENSE — add_license","text":"license character length 1. chosen license. Run get_licenses()) select appropriate one. given character length 1. given name copyright holder. required license = 'MIT'. NULL (default) license = 'MIT', function try retrieve value parameter .Rprofile file (edited set_credentials()). family character length 1. family name copyright holder. required license = 'MIT'. NULL (default) license = 'MIT', function try retrieve value parameter .Rprofile file (edited set_credentials()). quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a LICENSE — add_license","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a LICENSE — add_license","text":"","code":"if (FALSE) { add_license(license = \"MIT\") add_license(license = \"GPL (>= 2)\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a License badge — add_license_badge","title":"Add a License badge — add_license_badge","text":"function adds updates License badge README.Rmd. function reads License field DESCRIPTION file. Ensure field correctly defined. See add_license() detail. function requires presence DESCRIPTION file project root. See add_description() detail. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a License badge — add_license_badge","text":"","code":"add_license_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a License badge — add_license_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a License badge — add_license_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a License badge — add_license_badge","text":"","code":"if (FALSE) { add_license_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Life Cycle badge — add_lifecycle_badge","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"function adds updates Life Cycle badge README.Rmd. based standard defined https://lifecycle.r-lib.org/articles/stages.html. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"","code":"add_lifecycle_badge(lifecycle = \"experimental\", quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"lifecycle character length 1. Accepted stages : 'experimental' (default), 'stable', 'deprecated', 'superseded'. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"badge markdown expression.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"project can following life cycle stage: Experimental - experimental project made available user can try provide feedback, come promises long term stability. Stable - project considered stable author happy interface, see major issues, happy share world. Superseded - superseded project known better alternative, going away. Superseded project receive new features, receive critical bug fixes needed keep working. Deprecated - deprecated project better alternative available scheduled removal.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"","code":"if (FALSE) { add_lifecycle_badge() add_lifecycle_badge(lifecycle = \"stable\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Make-like R file — add_makefile","title":"Create a Make-like R file — add_makefile","text":"function creates Make-like R file (make.R) root project based template. used project research compendium. content file provides guidelines. See also new_compendium() information.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Make-like R file — add_makefile","text":"","code":"add_makefile(   given = NULL,   family = NULL,   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Make-like R file — add_makefile","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Make-like R file — add_makefile","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a Make-like R file — add_makefile","text":"","code":"if (FALSE) { add_makefile() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a package-level documentation file — add_package_doc","title":"Create a package-level documentation file — add_package_doc","text":"function adds package-level documentation file (pkg-package.R) R/ folder. file make help available user via ?pkg (pkg name package). good place put general directives like @import @importFrom.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a package-level documentation file — add_package_doc","text":"","code":"add_package_doc(open = TRUE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a package-level documentation file — add_package_doc","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a package-level documentation file — add_package_doc","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a package-level documentation file — add_package_doc","text":"","code":"if (FALSE) { add_package_doc() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":null,"dir":"Reference","previous_headings":"","what":"Add minimal R version to DESCRIPTION — add_r_depend","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"function adds minimal R version Depends field DESCRIPTION file. version corresponds higher version R among dependencies. dependencies mentions minimal R version, DESCRIPTION modified.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"","code":"add_r_depend()"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"","code":"if (FALSE) { add_r_depend() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a README file — add_readme_rmd","title":"Create a README file — add_readme_rmd","text":"function creates README.Rmd file root project based template. edited user needs knit README.md (use function refresh()).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a README file — add_readme_rmd","text":"","code":"add_readme_rmd(   type = \"package\",   given = NULL,   family = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a README file — add_readme_rmd","text":"type character length 1. package (default) GitHub README.Rmd specific R package created. compendium GitHub README.Rmd specific research compendium created. given character length 1. given name project maintainer. family character length 1. family name project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a README file — add_readme_rmd","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a README file — add_readme_rmd","text":"","code":"if (FALSE) { add_readme_rmd(type = \"package\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize renv — add_renv","title":"Initialize renv — add_renv","text":"function initializes renv environment project running renv::init(). See https://rstudio.github.io/renv/ detail.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize renv — add_renv","text":"","code":"add_renv(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize renv — add_renv","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize renv — add_renv","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize renv — add_renv","text":"","code":"if (FALSE) { add_renv() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Repository Status badge — add_repostatus_badge","title":"Add a Repository Status badge — add_repostatus_badge","text":"function adds updates Repository Status badge project README.Rmd. based standard defined https://www.repostatus.org project. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Repository Status badge — add_repostatus_badge","text":"","code":"add_repostatus_badge(status = \"concept\", quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Repository Status badge — add_repostatus_badge","text":"status character length 1. Accepted status : 'concept' (default), 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Repository Status badge — add_repostatus_badge","text":"badge markdown expression.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a Repository Status badge — add_repostatus_badge","text":"project can following status: Concept - Minimal implementation done yet, repository intended limited example, demo, proof--concept. WIP - Initial development progress, yet stable, usable release suitable public. Suspended - Initial development started, yet stable, usable release; work stopped time author(s) intend resuming work. Abandoned - Initial development started, yet stable, usable release; project abandoned author(s) intend continuing development. Active - project reached stable, usable state actively developed. Inactive - project reached stable, usable state longer actively developed; support/maintenance provided time allows. Unsupported - project reached stable, usable state author(s) ceased work . new maintainer may desired.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Repository Status badge — add_repostatus_badge","text":"","code":"if (FALSE) { add_repostatus_badge() add_repostatus_badge(status = \"active\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize units tests — add_testthat","title":"Initialize units tests — add_testthat","text":"function initializes units tests settings running usethis::use_testthat() adding example units tests file tests/testthat/test-demo.R. sample file test demo function created R/fun-demo.R.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize units tests — add_testthat","text":"","code":"add_testthat()"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize units tests — add_testthat","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize units tests — add_testthat","text":"","code":"if (FALSE) { add_testthat() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to the .Rbuildignore file — add_to_buildignore","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"function adds files/folders .Rbuildignore file. .Rbuildignore already present, files ignored checking package just added file. Otherwise new file created.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"","code":"add_to_buildignore(x, open = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"x character vector. One several files/folders names added .Rbuildignore. argument mandatory. open logical value. TRUE .Rbuildignore file opened editor. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"","code":"if (FALSE) { add_to_buildignore(open = TRUE) add_to_buildignore(\".DS_Store\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to the .gitignore file — add_to_gitignore","title":"Add to the .gitignore file — add_to_gitignore","text":"function creates .gitignore file root project based template (specific R). .gitignore already present, files untracked git just added file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to the .gitignore file — add_to_gitignore","text":"","code":"add_to_gitignore(x, open = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to the .gitignore file — add_to_gitignore","text":"x character vector. One several files/folders names added .gitignore. open logical value. TRUE .gitignore file opened editor. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add to the .gitignore file — add_to_gitignore","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add to the .gitignore file — add_to_gitignore","text":"","code":"if (FALSE) { add_to_gitignore(open = TRUE) add_to_gitignore(\".DS_Store\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a vignette document — add_vignette","title":"Create a vignette document — add_vignette","text":"function adds vignette folder vignettes/. also adds dependencies knitr rmarkdown field Suggests DESCRIPTION file (already present fields Imports).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a vignette document — add_vignette","text":"","code":"add_vignette(   filename = NULL,   title = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a vignette document — add_vignette","text":"filename character length 1. name .Rmd file created. NULL (default ) .Rmd file named pkg.Rmd pkg package name. title character length 1. title vignette. NULL (default) title Get started. open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a vignette document — add_vignette","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a vignette document — add_vignette","text":"","code":"if (FALSE) { ## Default vignette ---- add_vignette()  ## Default vignette ---- add_vignette(filename = \"pkg\", title = \"Get started\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all external dependencies — get_all_dependencies","title":"Get all external dependencies — get_all_dependencies","text":"function gets external packages project needs. used generate Dependencies badge (add_dependencies_badge()).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all external dependencies — get_all_dependencies","text":"","code":"get_all_dependencies(pkg = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all external dependencies — get_all_dependencies","text":"pkg character length 1. name CRAN package NULL (default). NULL get dependencies local (uninstalled) project (package compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all external dependencies — get_all_dependencies","text":"list three vectors: base_deps, vector base packages; direct_deps, vector direct packages; all_deps, vector dependencies (recursively obtained).","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get all external dependencies — get_all_dependencies","text":"","code":"if (FALSE) { ## Update dependencies ---- add_dependencies()  ## Get all dependencies ---- deps <- get_all_dependencies() unlist(lapply(deps, length))  ## Can be used for a CRAN package ---- deps <- get_all_dependencies(\"usethis\") unlist(lapply(deps, length)) }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"List all functions in the package — get_all_functions","title":"List all functions in the package — get_all_functions","text":"function returns list functions (exported internal) available package. function scans NAMESPACE R/ folder, recommended run devtools::document() .","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all functions in the package — get_all_functions","text":"","code":"get_all_functions()"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all functions in the package — get_all_functions","text":"list two vectors: external, vector exported functions name; internal, vector internal functions name.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all functions in the package — get_all_functions","text":"","code":"if (FALSE) { ## Update NAMESPACE ---- devtools::document()  ## List all implemented functions ---- get_all_functions() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":null,"dir":"Reference","previous_headings":"","what":"List all available licenses — get_licenses","title":"List all available licenses — get_licenses","text":"function returns list available licenses. particularly useful get right spelling license passed new_package(), new_compendium(), add_license().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all available licenses — get_licenses","text":"","code":"get_licenses()"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all available licenses — get_licenses","text":"data.frame following two variables: tag, license name used add_license(); url, URL license description.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all available licenses — get_licenses","text":"","code":"get_licenses() #>                      tag                                             url #> 1                    MIT        https://choosealicense.com/licenses/mit/ #> 2                    CC0    https://choosealicense.com/licenses/cc0-1.0/ #> 3              CC BY 4.0  https://choosealicense.com/licenses/cc-by-4.0/ #> 4                  GPL-2    https://choosealicense.com/licenses/gpl-2.0/ #> 5                  GPL-3    https://choosealicense.com/licenses/gpl-3.0/ #> 6             GPL (>= 2)    https://choosealicense.com/licenses/gpl-2.0/ #> 7             GPL (>= 3)    https://choosealicense.com/licenses/gpl-3.0/ #> 8               LGPL-2.1   https://choosealicense.com/licenses/lgpl-2.1/ #> 9                 LGPL-3   https://choosealicense.com/licenses/lgpl-3.0/ #> 10         LGPL (>= 2.1)   https://choosealicense.com/licenses/lgpl-2.1/ #> 11           LGPL (>= 3)   https://choosealicense.com/licenses/lgpl-3.0/ #> 12                AGPL-3   https://choosealicense.com/licenses/agpl-3.0/ #> 13           AGPL (>= 3)   https://choosealicense.com/licenses/agpl-3.0/ #> 14 Apache License (== 2) https://choosealicense.com/licenses/apache-2.0/ #> 15 Apache License (>= 2) https://choosealicense.com/licenses/apache-2.0/"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get required minimal R version — get_minimal_r_version","title":"Get required minimal R version — get_minimal_r_version","text":"function detects minimal required R version project based minimal required R version dependencies. can used update Depends field DESCRIPTION file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get required minimal R version — get_minimal_r_version","text":"","code":"get_minimal_r_version(pkg = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get required minimal R version — get_minimal_r_version","text":"pkg character length 1. name CRAN package NULL (default). NULL get minimal required R version local (uninstalled) project (package compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get required minimal R version — get_minimal_r_version","text":"character minimal required R version.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get required minimal R version — get_minimal_r_version","text":"","code":"if (FALSE) { ## Update dependencies ---- add_dependencies()  ## Minimal R version of a project ---- get_minimal_r_version()  ## Minimal R version of a CRAN package ---- get_minimal_r_version(\"usethis\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an R compendium structure — new_compendium","title":"Create an R compendium structure — new_compendium","text":"function creates research compendium (.e. predefined files/folders structure) help user organizing files/folders run analysis. addition common R packages files/folders (see new_package() information) function created following folders: data/: folder store raw data. Note data must never modified. user want modify recommended export new data outputs/. analyses/: folder write analyses instructions, .e. R scripts. user need create R functions recommended write R/ folder. outputs/: folder store intermediate final outputs generated R scripts. figures/: folder store figures generated R scripts. function also creates Make-like R file (make.R). file contains two main lines: devtools::install_deps(): downloads external dependencies required project (alternative install.packages()). Ideal sharing; devtools::load_all(): loads external dependencies R functions (alternative library() source() respectively). user writes R scripts /can add following line file: source(::(\"rscripts\", \"script_X.R\")). /can source entire make.R run analysis. function add_dependencies() can used automatically add external dependencies DESCRIPTION file. recommended, better reproducibility, call external dependencies pkg::fun() @import @importFrom R functions instead using library(). files/folders added .Rbuildignore rest project (e.g. R functions) can used (installed) R package.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an R compendium structure — new_compendium","text":"","code":"new_compendium(   compendium = NULL,   license = \"GPL (>= 2)\",   status = NULL,   lifecycle = NULL,   contributing = TRUE,   code_of_conduct = TRUE,   vignette = FALSE,   test = FALSE,   create_repo = TRUE,   private = FALSE,   gh_check = FALSE,   codecov = FALSE,   website = FALSE,   gh_render = FALSE,   gh_citation = FALSE,   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   renv = FALSE,   dockerfile = FALSE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an R compendium structure — new_compendium","text":"compendium character vector specifying folders created. See add_compendium() information. license character vector length 1. license used project. Run get_licenses() choose appropriate one. Default license = 'GPL (>= 2)' license can changed later calling add_license() (add_license_badge() refresh() update corresponding badge README). status character vector length 1. status project according standard defined https://www.repostatus.org project. One among 'concept', 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. See add_repostatus_badge() information. argument used add badge README.Rmd help visitors better understand project. Default status = NULL. status can added/changed later using add_repostatus_badge(). lifecycle character vector length 1. life cycle stage project according standard defined https://lifecycle.r-lib.org/articles/stages.html. One among 'experimental', 'stable', 'deprecated', 'superseded'. See add_lifecycle_badge() information. argument used add badge README.Rmd help visitors better understand project. Default lifecycle = NULL. stage can added/changed later using add_lifecycle_badge(). contributing logical value. TRUE (default) adds CONTRIBUTING.md file ISSUE_TEMPLATES. See add_contributing() information. code_of_conduct logical value. TRUE (default) adds CODE_OF_CONDUCT.md file. See add_code_of_conduct() information. vignette logical value. TRUE creates vignette vignettes/. Packages knitr rmarkdown also added Suggests field DESCRIPTION file. Default FALSE. test logical value. TRUE initializes units tests running usethis::use_testthat(). Package testthat also added Suggests field DESCRIPTION file. Default FALSE. create_repo logical value. TRUE (default) creates repository (public private = FALSE private private = TRUE) GitHub. See section Creating GitHub repo help page new_package(). private logical value. TRUE creates private repository user GitHub account (organisation). Default private = FALSE. gh_check logical value. TRUE configures GitHub Actions automatically check test package push. run R CMD check three major operating systems (Ubuntu, macOS, Windows) latest release R. See add_github_actions_check() information. create_repo = FALSE argument ignored. Default FALSE. codecov logical value. TRUE configures GitHub Actions automatically report code coverage units tests push. See add_github_actions_codecov() information. create_repo = FALSE argument ignored. Default FALSE. website logical value. TRUE configures GitHub Actions automatically build deploy package website (using pkgdown) push. gh-pages branch created using usethis::use_github_pages() GitHub repository automatically configured deploy website. create_repo = FALSE argument ignored. Default FALSE. gh_render logical value. TRUE configures GitHub Actions automatically knit README.Rmd push. See add_github_actions_render() information. create_repo = FALSE argument ignored. Default FALSE. gh_citation logical value. TRUE configures GitHub Actions automatically update CITATION.cff file. See add_github_actions_citation() information. create_repo = FALSE argument ignored. Default FALSE. given character vector length 1. given name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). family character vector length 1. family name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). email character vector length 1. email address maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). orcid character vector length 1. ORCID maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). organisation character vector length 1. GitHub organisation host repository. defined overwrite GitHub pseudo. Default organisation = NULL (GitHub pseudo used). renv logical value. TRUE initializes renv environment project running renv::init(). Package renv also added Imports field DESCRIPTION file. Default FALSE. dockerfile logical value. TRUE creates Dockerfile project. See add_dockerfile() detail. Default FALSE. overwrite logical value. TRUE files written templates modified user erased. Default overwrite = FALSE. careful using argument. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an R compendium structure — new_compendium","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an R compendium structure — new_compendium","text":"","code":"if (FALSE) { library(rcompendium)  ## Define **ONCE FOR ALL** your credentials ---- set_credentials(given = \"John\", family = \"Doe\",                  email = \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")  ## Create an R package ---- new_compendium()  ## Start adding data and developing functions and scripts ---- ## ...  ## Update package (documentation, dependencies, README, check) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an R package structure — new_package","title":"Create an R package structure — new_package","text":"function creates new R package structure according current best practices. Essential features R package created (DESCRIPTION NAMESPACE files, R/ man/ folders). project also versioned git generic R .gitignore added. IMPORTANT - using function user needs create new folder (new project using RStudio) run function inside folder (using setwd() opening Rproj new RStudio session). name package name folder. rules must respected: https://r-pkgs.org/workflow101.html#name--package. fields DESCRIPTION file (maintainer information, package name, license, URLs,  roxygen2 version)  automatically filled others (like title description) need edited manually. Additional features also created: CITATION file, README.Rmd, tests/ vignettes/ folders (optional). See vignette Get started complete overview full structure. GitHub repository can also created (default) following \"GitHub last\" workflow (https://happygitwithr.com/existing-github-last.html). Configuration files GitHub Actions automatically 1) check package, 2) test report code coverage, 3) deploy website using pkgdown added .github/ folder. See section Creating GitHub repo.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an R package structure — new_package","text":"","code":"new_package(   license = \"GPL (>= 2)\",   status = NULL,   lifecycle = NULL,   contributing = TRUE,   code_of_conduct = TRUE,   vignette = TRUE,   test = TRUE,   create_repo = TRUE,   private = FALSE,   gh_check = TRUE,   codecov = TRUE,   website = TRUE,   gh_render = TRUE,   gh_citation = TRUE,   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an R package structure — new_package","text":"license character vector length 1. license used package. Run get_licenses() choose appropriate one. Default license = 'GPL (>= 2)' license can changed later calling add_license() (add_license_badge() refresh() update corresponding badge README). status character vector length 1. status project according standard defined  https://www.repostatus.org project. One among 'concept', 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. See add_repostatus_badge() information. argument used add badge README.Rmd help visitors better understand project. want badge use status = NULL (default). status can added/changed later using add_repostatus_badge(). lifecycle character vector length 1. life cycle stage project according standard defined https://lifecycle.r-lib.org/articles/stages.html. One among 'experimental', 'stable', 'deprecated', 'superseded'. See add_lifecycle_badge() information. argument used add badge README.Rmd help visitors better understand project. want badge use lifecycle = NULL (default). stage can added/changed later using add_lifecycle_badge(). contributing logical value. TRUE (default) adds CONTRIBUTING.md file ISSUE_TEMPLATES. See add_contributing() information. code_of_conduct logical value. TRUE (default) adds CODE_OF_CONDUCT.md file. See add_code_of_conduct() information. vignette logical value. TRUE (default) creates vignette vignettes/. Packages knitr rmarkdown also added Suggests field DESCRIPTION file. test logical value. TRUE (default) initializes units tests running usethis::use_testthat(). Package testthat also added Suggests field DESCRIPTION file. create_repo logical value. TRUE (default) creates repository (public private = FALSE private private = TRUE) GitHub. See section Creating GitHub repo. private logical value. TRUE creates private repository user GitHub account (organisation). Default private = FALSE. gh_check logical value. TRUE (default) configures GitHub Actions automatically check test package push. run R CMD check three major operating systems (Ubuntu, macOS, Windows) latest release R. See add_github_actions_check() information. create_repo = FALSE argument ignored. codecov logical value. TRUE (default) configures GitHub Actions automatically report code coverage units tests push. See add_github_actions_codecov() information. create_repo = FALSE argument ignored. website logical value. TRUE (default) configures GitHub Actions automatically build deploy package website (using pkgdown) push. gh-pages branch created using usethis::use_github_pages() GitHub repository automatically configured deploy website. create_repo = FALSE argument ignored. gh_render logical value. TRUE (default) configures GitHub Actions automatically knit README.Rmd push. See add_github_actions_render() information. create_repo = FALSE argument ignored. gh_citation logical value. TRUE (default) configures GitHub Actions automatically update CITATION.cff file. See add_github_actions_citation() information. create_repo = FALSE argument ignored. given character vector length 1. given name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. family character vector length 1. family name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. email character vector length 1. email address maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. orcid character vector length 1. ORCID maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. organisation character vector length 1. GitHub organisation host repository. defined overwrite GitHub pseudo. Default organisation = NULL (GitHub pseudo used). overwrite logical value. TRUE files written templates modified user erased. Default overwrite = FALSE. careful using argument. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an R package structure — new_package","text":"return value.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"recommended-workflow","dir":"Reference","previous_headings":"","what":"Recommended workflow","title":"Create an R package structure — new_package","text":"purpose package rcompendium make easier creation R package/research compendium user can focus code/analysis instead wasting time organizing files. recommended workflow : Create empty RStudio project; Store credentials set_credentials() (already done); Run new_package() create new package structure (GitHub repository); Edit metadata DESCRIPTION, CITATION, README.Rmd; Implement, document & test functions (fun part); Update project (update .Rd files, NAMESPACE, external dependencies DESCRIPTION, re-knit README.Rmd, check package integrity) refresh(); Repeat steps 5 6 developing package.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"managing-credentials","dir":"Reference","previous_headings":"","what":"Managing credentials","title":"Create an R package structure — new_package","text":"can use arguments given, family, email, orcid directly function new_package() (others). create lot projects (packages /compendiums) can frustrating long run. alternative use function set_credentials() permanently store information .Rprofile file. arguments set NULL (default) function package rcompendium search .Rprofile file. save time (purpose package). Even stored information .Rprofile file always able modify --fly (.e. using arguments new_package()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"configuring-git","dir":"Reference","previous_headings":"","what":"Configuring git","title":"Create an R package structure — new_package","text":"First run gh::gh_whoami() see git correctly configured. see something like:   Otherwise might need run:   See gert::git_config_global_set() information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name  = \"user.name\",                              value = \"John Doe\")                              gert::git_config_global_set(name  = \"user.email\",                              value = \"john.doe@domain.com\")                              gert::git_config_global_set(name  = \"github.user\",                              value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"creating-a-github-repo","dir":"Reference","previous_headings":"","what":"Creating a GitHub repo","title":"Create an R package structure — new_package","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). GITHUB PAT locally stored, must: Obtain new one GitHub account. Make sure select least first two scopes (private repository workflow) Store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9' Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured see something like calling gh::gh_whoami():   able create GitHub repository directly R!","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"delete_repo, repo, workflow\",   \"token\": \"ghp_99z9...z9\" }"},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an R package structure — new_package","text":"","code":"if (FALSE) { library(rcompendium)  ## Define **ONCE FOR ALL** your credentials ---- set_credentials(given = \"John\", family = \"Doe\",                  email = \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")  ## Create an R package ---- new_package()  ## Start developing functions ---- ## ...  ## Update package (documentation, dependencies, README, check) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a package or research compendium structure — rcompendium-package","title":"Create a package or research compendium structure — rcompendium-package","text":"rcompendium makes easier creation R packages research compendia (.e. predefined files/folders structure) users can focus code/analysis instead wasting time organizing files. full ready--work structure set additional features: version control, remote repository creation, CI/CD configuration (check package integrity several OS, test code 'testthat', build deploy website using 'pkgdown').","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"recommended-workflow","dir":"Reference","previous_headings":"","what":"Recommended workflow","title":"Create a package or research compendium structure — rcompendium-package","text":"Store credentials (given family names, email, ORCID, etc.) set_credentials() (already done); Create new empty RStudio project; Run new_package() create new package structure new_compendium() create new research compendium structure; Edit metadata DESCRIPTION, CITATION, README.Rmd; Start working (add data, write document R functions, etc.); forget commit changes.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"managing-credentials","dir":"Reference","previous_headings":"","what":"Managing credentials","title":"Create a package or research compendium structure — rcompendium-package","text":"can use arguments given, family, email, orcid directly functions new_*() add_*(). create lot projects (packages /compendia) can frustrating long run. alternative way use function set_credentials() permanently store information ~/.Rprofile file. arguments set NULL calling function package, rcompendium search values file. save time (purpose package). Even stored credentials ~/.Rprofile file always able modify --fly (.e. using credentials arguments functions new_*() add_*()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"configuring-git","dir":"Reference","previous_headings":"","what":"Configuring git","title":"Create a package or research compendium structure — rcompendium-package","text":"see git correctly configured laptop, run gh::gh_whoami(). see something like:   Otherwise might need run:   See gert::git_config_global_set() information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name  = \"user.name\",                              value = \"John Doe\")                              gert::git_config_global_set(name  = \"user.email\",                              value = \"john.doe@domain.com\")                              gert::git_config_global_set(name  = \"github.user\",                              value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"creating-a-github-repo","dir":"Reference","previous_headings":"","what":"Creating a GitHub repo","title":"Create a package or research compendium structure — rcompendium-package","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). GITHUB PAT locally stored, must: Visit page https://github.com/settings/tokens create new token; Store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9'. Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured, see something like calling gh::gh_whoami():","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"repo, workflow\",   \"token\": \"ghp_...z99Z\" }"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"resources","dir":"Reference","previous_headings":"","what":"Resources","title":"Create a package or research compendium structure — rcompendium-package","text":"Developing R package: https://frbcesab.github.io/rcompendium/articles/developing_a_package.html Working compendium: https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create a package or research compendium structure — rcompendium-package","text":"Maintainer: Nicolas Casajus nicolas.casajus@fondationbiodiversite.fr (ORCID) [copyright holder]","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":null,"dir":"Reference","previous_headings":"","what":"Refresh a package/research compendium — refresh","title":"Refresh a package/research compendium — refresh","text":"function removed rcompendium. function refreshes package/research compendium. : Update .Rd files NAMESPACE using devtools::document(); Update external packages (DESCRIPTION file) using add_dependencies(); Update badges README.Rmd (already present); Re-knitr README.Rmd using rmarkdown::render(); Check package integrity using devtools::check(); Run analysis sourcing make.R (compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Refresh a package/research compendium — refresh","text":"","code":"refresh(compendium = NULL, make = FALSE, check = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Refresh a package/research compendium — refresh","text":"compendium character length 1. name folder recursively detect dependencies added Imports field DESCRIPTION file. can 'analysis/' (additional folders, .e. data/, outputs/, figures/, etc. created folder), '.' (folders data/, outputs/, figures/, etc. created root project), etc. See new_compendium() information. Default compendium = NULL (.e. additional folder inspected R/, NAMESPACE, vignettes/, tests/ still inspected). make logical value. TRUE Make-like R file make.R sourced. research compendium created new_compendium(). Default FALSE. check logical value. TRUE package integrity checked using devtools::check(). Default FALSE. quiet logical value. TRUE (default) message deleted.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Refresh a package/research compendium — refresh","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Refresh a package/research compendium — refresh","text":"","code":"if (FALSE) { library(rcompendium)  ## Create an R package ---- new_package()  ## Start developing functions ---- ## ...  ## Update package (documentation, dependencies, README) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":null,"dir":"Reference","previous_headings":"","what":"Store credentials to the .Rprofile — set_credentials","title":"Store credentials to the .Rprofile — set_credentials","text":"function used store user credentials .Rprofile file. Accepted credentials listed . function useful user creates lot packages /research compendiums. .Rprofile file exist function create . Users need paste content clipboard file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Store credentials to the .Rprofile — set_credentials","text":"","code":"set_credentials(   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   protocol = NULL )"},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Store credentials to the .Rprofile — set_credentials","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. orcid character length 1. ORCID project maintainer. protocol character length 1. GIT protocol used communicate GitHub remote. One 'https' 'ssh'. know, keep default value (.e. NULL) protocol 'https'.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Store credentials to the .Rprofile — set_credentials","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Store credentials to the .Rprofile — set_credentials","text":"","code":"if (FALSE) { library(rcompendium)   ## Define **ONCE FOR ALL** your credentials ----  set_credentials(\"John\", \"Doe\", \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"https\") }"},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-13","dir":"Changelog","previous_headings":"","what":"rcompendium 1.3","title":"rcompendium 1.3","text":"CRAN release: 2023-10-26 Bug fixes get_deps_*() better detects project dependencies delete packages called w/ library(\"pkg\") library('pkg') add_sticker() now copies sticker template compendium Minor changes Provide instructions installing V8 engine Unix systems","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-12","dir":"Changelog","previous_headings":"","what":"rcompendium 1.2","title":"rcompendium 1.2","text":"CRAN release: 2023-10-24 New features get_git_branch_name() detects git branch name add_contributing() adds CONTRIBUTING.md file issue templates add_code_of_conduct() adds CODE_OF_CONDUCT.md file add_github_actions_citation() adds new GitHub action update CITATION.cff file add_github_actions_document() adds new GitHub action update Rd files, NAMESPACE DESCRIPTION files Improvements get_deps_*() better detects project dependencies add_compendium() allows now user choose compendium structure Minor changes Update GitHub Actions templates (yaml files) Update README templates man/ folder NAMESPACE now untracked git (compendium ) Remove dependencies badge README Change default values lifecycle status arguments new_package() Change commit messages new_*() functions (conventional commits) Deprecated refresh() now deprecated deleted new version","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-11","dir":"Changelog","previous_headings":"","what":"rcompendium 1.1","title":"rcompendium 1.1","text":"CRAN release: 2023-04-24 Update GitHub Actions templates (yaml files) Detect current git branch name add_readme_rmd() Ignore renv files (R build GitHub) add_renv()","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-10","dir":"Changelog","previous_headings":"","what":"rcompendium 1.0","title":"rcompendium 1.0","text":"CRAN release: 2022-04-06 New feature: add_dockerfile() creates basic Dockerfile compendium (new argument dokerfile new_compendium()) based rocker/rstudio. New feature: add_renv() initialize renv environment compendium (new argument renv new_compendium()) New feature: add_github_actions_render() automatically render README.md GitHub server push. action triggered README.Rmd modified since last commit. Also add new argument gh_render new_*() functions. New vignette: developing R package New vignette: working compendium Function add_dependencies() allows now missing R/ folder improves detection dependencies vignettes. Function add_lifecycle_badge() copy badge SVG project anymore. image badge now created using https://shields.io/. Update GHA templates. now derived : https://github.com/r-lib/actions/tree/v2-branch/examples Rename default vignette title (title now Get Started) Add cph (copyright holder) tag DESCRIPTION file Change default package hexSticker add R script inst/package-sticker/ easily change hexSticker Rename commits messages (remove emoji) compendium: arguments gh_check website now FALSE default compendium: rename rscripts/ folder analyses/ compendium: delete paper/ folder Review improve documentation Rename templates file names Fix bug: detection nested RStudio projects","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-051","dir":"Changelog","previous_headings":"","what":"rcompendium 0.5.1","title":"rcompendium 0.5.1","text":"CRAN release: 2021-03-24 first submission CRAN: DESCRIPTION file: replace “aim package ‘rcompendium’ make easier…” “Makes easier…” Function set_credentials() write .Rprofile file anymore (allowed CRAN policies). Instead function opens file users need manually paste content clipboard. Replace utils::installed.packages() find.package()","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-05","dir":"Changelog","previous_headings":"","what":"rcompendium 0.5","title":"rcompendium 0.5","text":"Check valid package name Add new features: new_compendium() add_compendium() Allow adding .gitignore .Rbuildignore several names Improve console messages Modify templates","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-041","dir":"Changelog","previous_headings":"","what":"rcompendium 0.4.1","title":"rcompendium 0.4.1","text":"Improve documentation","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-04","dir":"Changelog","previous_headings":"","what":"rcompendium 0.4","title":"rcompendium 0.4","text":"New features: add_testthat(), add_github_actions_codecov(), add_github_actions_codecov_badge(), add_codecov_badge() New arguments new_package(): test codecov Add demo R function pass test show good practices writing functions","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-03","dir":"Changelog","previous_headings":"","what":"rcompendium 0.3","title":"rcompendium 0.3","text":"Improve dependencies detection @examples sections Keep packages versions DESCRIPTION fields Retrieve GitHub pseudo gh::gh_whoami() (github argument)","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-02","dir":"Changelog","previous_headings":"","what":"rcompendium 0.2","title":"rcompendium 0.2","text":"Rename import argument compendium Automatically check dependencies vignettes/ (remove argument suggest) Detect dependencies tests/ Add new internal function path_proj() Use usethis::proj_get() instead ::() Rename add_github_badge() add_github_actions_check_badge() Add new function add_github_actions_pkgdown_badge() Badge functions return now Markdown badges (assigned variable) Badges added end process (adding additional commit) Change default license new_package() Improve inputs checks Change files templates (GH Actions names)","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-01","dir":"Changelog","previous_headings":"","what":"rcompendium 0.1","title":"rcompendium 0.1","text":"First release package.","code":""}]
+[{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement nicolas.casajus@fondationbiodiversite.fr. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to rcompendium","title":"Contributing to rcompendium","text":"First , thanks taking time contribute rcompendium! types contributions encouraged valued. See Table contents different ways help details project handles . Please make sure read relevant section making contribution. make lot easier us maintainers smooth experience involved.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contributing to rcompendium","text":"Code conduct Style guide Commit messages Asking questions Reporting bugs Requesting features Contributing code","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of conduct","title":"Contributing to rcompendium","text":"project released Contributor Code Conduct. participating, expected uphold code. Please report unacceptable behavior nicolas.casajus@fondationbiodiversite.fr.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"","what":"Style guide","title":"Contributing to rcompendium","text":"use Tidyverse style guide writing R code. Functions documented roxygen2 syntax. rcompendium uses lower_snake_case.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"commit-messages","dir":"","previous_headings":"","what":"Commit messages","title":"Contributing to rcompendium","text":"want contribute commiting changes, please try use Conventional commits specification.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"asking-questions","dir":"","previous_headings":"","what":"Asking questions","title":"Contributing to rcompendium","text":"ask question, best search existing Issues might help . case found suitable issue still need clarification, can write question issue. still feel need ask question need clarification, recommend following: Open new Issue. Use template other_issue.md. Provide much context can ’re running . Provide project platform versions (paste output sessionInfo()). take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"before-submitting-a-bug-report","dir":"","previous_headings":"Reporting bugs","what":"Before submitting a bug report","title":"Contributing to rcompendium","text":"good bug report shouldn’t leave others needing chase information. Therefore, ask investigate carefully, collect information describe issue detail report. Please complete following steps advance help us fix potential bug fast possible. Make sure using latest version rcompendium. Determine bug really bug error side. see users experienced (potentially already solved) issue , check already bug report existing bug error bug tracker.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"how-do-i-submit-a-bug-report","dir":"","previous_headings":"Reporting bugs","what":"How do I submit a bug report?","title":"Contributing to rcompendium","text":"use GitHub Issues track bugs errors. run issue project: Open new Issue. Use template bug_report.md. Explain behavior expect actual behavior. Please provide much context possible describe reproduction steps someone else can follow recreate issue . usually includes code reproducible example. take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"before-requesting-a-feature","dir":"","previous_headings":"Requesting features","what":"Before requesting a feature","title":"Contributing to rcompendium","text":"Make sure using latest version rcompendium. Read documentation carefully find functionality already covered. Perform search see enhancement already suggested. , add comment existing issue instead opening new one.","code":""},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"how-do-i-submit-a-feature-request","dir":"","previous_headings":"Requesting features","what":"How do I submit a feature request?","title":"Contributing to rcompendium","text":"Feature requests tracked GitHub Issues. Open new Issue. Use template feature_request.md. Provide clear descriptive title issue identify suggestion. Provide step--step description suggested enhancement many details possible. Explain enhancement useful rcompendium users. take care issue soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"general-workflow","dir":"","previous_headings":"Contributing code","what":"General workflow","title":"Contributing to rcompendium","text":"use GitHub flow collaborate project: Fork repository using GitHub interface. Clone fork using git clone fork-url (replace fork-url URL fork). Alternatively, open RStudio IDE create New Project Version Control. Create new branch w/ git checkout -b branch-name (replace branch-name name new branch). Make contribution (see examples). Stage (git add) commit (git commit) changes often necessary Push changes GitHub w/ git push origin branch-name. Submit Pull Request original repo. review PR soon possible.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-the-readme","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing the README","title":"Contributing to rcompendium","text":"want contribute improving README, please edit README.Rmd (README.md). forget update README.md running:","code":"rmarkdown::render(\"README.Rmd\")"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-vignettes","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing vignettes","title":"Contributing to rcompendium","text":"want contribute editing existing vignette, just edit corresponding Rmd file stored vignettes/ folder. want contribute adding new vignette, create new Rmd file vignettes/ folder add following header: use new external dependency, forget add DESCRIPTION file section Suggests (package already listed section Imports). Check integrity package :","code":"--- title: \"Vignette Title\" output: rmarkdown::html_vignette vignette: >   %\\VignetteIndexEntry{Vignette Title}   %\\VignetteEngine{knitr::rmarkdown}   %\\VignetteEncoding{UTF-8} --- devtools::check()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"editing-function-documentation","dir":"","previous_headings":"Contributing code > Improve documentation","what":"Editing function documentation","title":"Contributing to rcompendium","text":"want contribute improving documentation function, open corresponding file R/ folder edit lines starting #' (roxygen2 syntax). Update documentation (Rd files man/ folder) running: use new external dependency example section, forget add DESCRIPTION file section Imports (package already listed). Check integrity package :","code":"devtools::document() devtools::check()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"fix-bug","dir":"","previous_headings":"Contributing code","what":"Fix bug","title":"Contributing to rcompendium","text":"want contribute improving code function, open edit corresponding file R/ folder. Check integrity package : forget adapt unit tests function editing corresponding file stored tests/testthat/ folder. use package testthat implement unit tests. Check tests running:","code":"devtools::check() devtools::test()"},{"path":"https://frbcesab.github.io/rcompendium/CONTRIBUTING.html","id":"new-feature","dir":"","previous_headings":"Contributing code","what":"New feature","title":"Contributing to rcompendium","text":"want contribute submitting new feature, please follow workflow: Create new R file folder R/. Implement code function. Document function w/ roxygen2 syntax. necessary, add additional dependencies DESCRIPTION file. Update package documentation w/ devtools::document(). Create new R file folder tests/testthat/. Implement unit tests new function. Check integrity package w/ devtools::check(). Thanks contribution!","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 2, June 1991Copyright © 1989, 1991 Free Software Foundation, Inc.,51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"licenses software designed take away freedom share change . contrast, GNU General Public License intended guarantee freedom share change free software–make sure software free users. General Public License applies Free Software Foundation’s software program whose authors commit using . (Free Software Foundation software covered GNU Lesser General Public License instead.) can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge service wish), receive source code can get want , can change software use pieces new free programs; know can things. protect rights, need make restrictions forbid anyone deny rights ask surrender rights. restrictions translate certain responsibilities distribute copies software, modify . example, distribute copies program, whether gratis fee, must give recipients rights . must make sure , , receive can get source code. must show terms know rights. protect rights two steps: (1) copyright software, (2) offer license gives legal permission copy, distribute /modify software. Also, author’s protection , want make certain everyone understands warranty free software. software modified someone else passed , want recipients know original, problems introduced others reflect original authors’ reputations. Finally, free program threatened constantly software patents. wish avoid danger redistributors free program individually obtain patent licenses, effect making program proprietary. prevent , made clear patent must licensed everyone’s free use licensed . precise terms conditions copying, distribution modification follow.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"terms-and-conditions-for-copying-distribution-and-modification","dir":"","previous_headings":"","what":"TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION","title":"GNU General Public License","text":"0. License applies program work contains notice placed copyright holder saying may distributed terms General Public License. “Program”, , refers program work, “work based Program” means either Program derivative work copyright law: say, work containing Program portion , either verbatim modifications /translated another language. (Hereinafter, translation included without limitation term “modification”.) licensee addressed “”. Activities copying, distribution modification covered License; outside scope. act running Program restricted, output Program covered contents constitute work based Program (independent made running Program). Whether true depends Program . 1. may copy distribute verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice disclaimer warranty; keep intact notices refer License absence warranty; give recipients Program copy License along Program. may charge fee physical act transferring copy, may option offer warranty protection exchange fee. 2. may modify copy copies Program portion , thus forming work based Program, copy distribute modifications work terms Section 1 , provided also meet conditions: ) must cause modified files carry prominent notices stating changed files date change. b) must cause work distribute publish, whole part contains derived Program part thereof, licensed whole charge third parties terms License. c) modified program normally reads commands interactively run, must cause , started running interactive use ordinary way, print display announcement including appropriate copyright notice notice warranty (else, saying provide warranty) users may redistribute program conditions, telling user view copy License. (Exception: Program interactive normally print announcement, work based Program required print announcement.) requirements apply modified work whole. identifiable sections work derived Program, can reasonably considered independent separate works , License, terms, apply sections distribute separate works. distribute sections part whole work based Program, distribution whole must terms License, whose permissions licensees extend entire whole, thus every part regardless wrote . Thus, intent section claim rights contest rights work written entirely ; rather, intent exercise right control distribution derivative collective works based Program. addition, mere aggregation another work based Program Program (work based Program) volume storage distribution medium bring work scope License. 3. may copy distribute Program (work based , Section 2) object code executable form terms Sections 1 2 provided also one following: ) Accompany complete corresponding machine-readable source code, must distributed terms Sections 1 2 medium customarily used software interchange; , b) Accompany written offer, valid least three years, give third party, charge cost physically performing source distribution, complete machine-readable copy corresponding source code, distributed terms Sections 1 2 medium customarily used software interchange; , c) Accompany information received offer distribute corresponding source code. (alternative allowed noncommercial distribution received program object code executable form offer, accord Subsection b .) source code work means preferred form work making modifications . executable work, complete source code means source code modules contains, plus associated interface definition files, plus scripts used control compilation installation executable. However, special exception, source code distributed need include anything normally distributed (either source binary form) major components (compiler, kernel, ) operating system executable runs, unless component accompanies executable. distribution executable object code made offering access copy designated place, offering equivalent access copy source code place counts distribution source code, even though third parties compelled copy source along object code. 4. may copy, modify, sublicense, distribute Program except expressly provided License. attempt otherwise copy, modify, sublicense distribute Program void, automatically terminate rights License. However, parties received copies, rights, License licenses terminated long parties remain full compliance. 5. required accept License, since signed . However, nothing else grants permission modify distribute Program derivative works. actions prohibited law accept License. Therefore, modifying distributing Program (work based Program), indicate acceptance License , terms conditions copying, distributing modifying Program works based . 6. time redistribute Program (work based Program), recipient automatically receives license original licensor copy, distribute modify Program subject terms conditions. may impose restrictions recipients’ exercise rights granted herein. responsible enforcing compliance third parties License. 7. , consequence court judgment allegation patent infringement reason (limited patent issues), conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. distribute satisfy simultaneously obligations License pertinent obligations, consequence may distribute Program . example, patent license permit royalty-free redistribution Program receive copies directly indirectly , way satisfy License refrain entirely distribution Program. portion section held invalid unenforceable particular circumstance, balance section intended apply section whole intended apply circumstances. purpose section induce infringe patents property right claims contest validity claims; section sole purpose protecting integrity free software distribution system, implemented public license practices. Many people made generous contributions wide range software distributed system reliance consistent application system; author/donor decide willing distribute software system licensee impose choice. section intended make thoroughly clear believed consequence rest License. 8. distribution /use Program restricted certain countries either patents copyrighted interfaces, original copyright holder places Program License may add explicit geographical distribution limitation excluding countries, distribution permitted among countries thus excluded. case, License incorporates limitation written body License. 9. Free Software Foundation may publish revised /new versions General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies version number License applies “later version”, option following terms conditions either version later version published Free Software Foundation. Program specify version number License, may choose version ever published Free Software Foundation. 10. wish incorporate parts Program free programs whose distribution conditions different, write author ask permission. software copyrighted Free Software Foundation, write Free Software Foundation; sometimes make exceptions . decision guided two goals preserving free status derivatives free software promoting sharing reuse software generally.","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"no-warranty","dir":"","previous_headings":"","what":"NO WARRANTY","title":"GNU General Public License","text":"11. PROGRAM LICENSED FREE CHARGE, WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION. 12. EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MAY MODIFY /REDISTRIBUTE PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES. END TERMS CONDITIONS","code":""},{"path":"https://frbcesab.github.io/rcompendium/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively convey exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program interactive, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, commands use may called something show w show c; even mouse-clicks menu items–whatever suits program. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. sample; alter names: General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker.  <signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice"},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"package-content","dir":"Articles","previous_headings":"","what":"Package content","title":"Developing an R package","text":"First, create new empty RStudio project. Let’s called pkg. create new package structure, run rcompendium::new_package(). default, following content created:  addition, new GitHub repository created directly R. available : https://github.com/{{account}}/pkg/ ({{account}} either GitHub account GitHub organization). minutes later, website (pkgdown) deployed : https://{{account}}.github.io/pkg/.","code":"pkg/                              # Root of the package │ ├── pkg.Rproj                     # RStudio project (created by user, optional) │ ├── .git/                         # GIT tracking folder ├── .gitignore                    # List of files/folders to be ignored by GIT |                                 # (specific to R language) | ├── .github/                      # (optional) GitHub Actions settings │   └── workflows/ │       ├── pkgdown.yaml          # Configuration file to build & deploy website │       ├── R-CMD-check.yaml      # Configuration file to check & test package │       ├── render-README.yaml    # Configuration file to render the README.md │       └── test-coverage.yaml    # Configuration file to report code coverage │ ├── _pkgdown.yaml                 # (optional) User website settings │ ├── R/                            # R functions location │   ├── fun-demo.R                # Example of an R function (to remove) │   └── pkg-package.R             # Dummy R file for package-level documentation │ ├── man/                          # R functions helps (automatically updated) │   ├── print_msg.Rd              # Documentation of the demo R function │   ├── pkg-package.Rd            # Package-level documentation │   └── figures/                  # Figures for the README  │       └── package-sticker.png   # Package sticker template │ ├── tests/                        # (optional) Units tests location │   ├── testthat.R                # Units tests settings │   └── testthat/                 # Units tests location │       └── test-demo.R           # Units tests for the demo function (to remove) | ├── vignettes/                    # (optional) Vignettes location │   └── pkg.Rmd                   # Get started tutorial                          [*] │ ├── DESCRIPTION                   # Project metadata                              [*] ├── LICENSE.md                    # Content of the GPL (>= 2) license (default) ├── NAMESPACE                     # Automatically generated ├── .Rbuildignore                 # List of files/folders to be ignored while  │                                 # checking/installing the package ├── inst/ │   ├── CITATION                  # BiBTeX entry to cite the package              [*] │   └── package-sticker/ │       ├── package-sticker.R     # Code to generate package sticker │       └── r_logo.png            # R logo │ ├── README.md                     # GitHub README (automatically generated) └── README.Rmd                    # GitHub README                                 [*]   [*] These files are automatically created but user needs to manually add      some information."},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"description","dir":"Articles","previous_headings":"Package metadata","what":"DESCRIPTION","title":"Developing an R package","text":"DESCRIPTION file contains important package metadata. default, rcompendium creates following file: information, please read https://r-pkgs.org/description.html. N.B. change Title, Description, Version, Authors@R values, forget also change citation information inst/CITATION README.Rmd.","code":"Package: pkg Type: Package Title: The Title of the Project                                              [*] Version: 0.0.0.9000 Authors@R: c(     person(given   = \"John\",            family  = \"Doe\",            role    = c(\"aut\", \"cre\", \"cph\"),            email   = \"john.doe@domain.com\",            comment = c(ORCID = \"9999-9999-9999-9999\"))) Description: A paragraph providing a full description of the project (on     [*]      several lines...) URL: https://github.com/jdoe/pkg BugReports: https://github.com/jdoe/pkg/issues License: GPL (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 VignetteBuilder: knitr Suggests:      knitr,     rmarkdown,     testthat (>= 3.0.0) Config/testthat/edition: 3   [*] Title and Description must be adapted by user."},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"readme","dir":"Articles","previous_headings":"Package metadata","what":"README","title":"Developing an R package","text":"README.md homepage repository GitHub. purpose help visitor understand project. Always edit README.Rmd (.md version). information, please read https://r-pkgs.org/release.html#readme.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"recommended-workflow","dir":"Articles","previous_headings":"","what":"Recommended workflow","title":"Developing an R package","text":"recommended workflow : Implement new function R/ Document function using roxygen syntax Update functions doc (man/) NAMESPACE devtools::document() Update list required packages DESCRIPTION rcompendium::add_dependencies() Implement units tests using testthat Edit vignette illustrate new feature Check test package devtools::check() can also provide data package. See ?usethis::use_data.  strongly recommend read book R packages Hadley Wickham Jenny Bryan.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/developing_a_package.html","id":"resources","dir":"Articles","previous_headings":"","what":"Resources","title":"Developing an R package","text":"R packages Hadley Wickham Jenny Bryan Writing R extensions R Development Core Team Extending R John M. Chambers","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"prerequisites","dir":"Articles","previous_headings":"","what":"Prerequisites","title":"Get started with rcompendium","text":"using package rcompendium must follow three steps.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"git-configuration","dir":"Articles","previous_headings":"Prerequisites","what":"GIT configuration","title":"Get started with rcompendium","text":"First ensure GIT correctly installed machine linked RStudio. Read Chapter 6 Happy Git GitHub useR. also need store GIT credentials locally (.e. project) globally (recommended). Run gh::gh_whoami() see git associated credentials correctly configured. see something like: Otherwise might need run: See ?gert::git_config_global_set information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name = \"user.name\",   value = \"John Doe\") gert::git_config_global_set(name = \"user.email\",  value = \"john.doe@domain.com\") gert::git_config_global_set(name = \"github.user\", value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"creating-a-github-repo","dir":"Articles","previous_headings":"Prerequisites","what":"Creating a GitHub repo","title":"Get started with rcompendium","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). don’t GITHUB PAT locally stored, must: visit page https://github.com/settings/tokens create new token; store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9'. Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured, see something like calling gh::gh_whoami(): able create GitHub repository directly R!","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"delete_repo, repo, workflow\",   \"token\": \"ghp_99z9...z9\" }"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"managing-credentials","dir":"Articles","previous_headings":"Prerequisites","what":"Managing credentials","title":"Get started with rcompendium","text":"can use arguments given, family, email, orcid directly functions new_*() add_*(). create lot projects (packages /compendia) can frustrating long run. alternative way use function set_credentials() permanently store information ~/.Rprofile file. arguments set NULL calling function package, rcompendium search values file. save time (’s purpose package). Even stored credentials ~/.Rprofile file always able modify --fly (.e. using credentials arguments functions new_*() add_*()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"usage","dir":"Articles","previous_headings":"","what":"Usage","title":"Get started with rcompendium","text":"recommended workflow : Store credentials set_credentials() (already done); IMPORTANT - Create new empty RStudio project; Run new_package() create new package structure new_compendium() create new research compendium structure; Edit metadata DESCRIPTION, CITATION, README.Rmd; Start working (add data, write document R functions, etc.); forget commit changes.  addition three setup functions (set_credentials(), new_package(), new_compendium()), package rcompendium offers 29 functions. can grouped : add_*(): functions add/update/overwrite files, configuration settings, dependencies, badges, etc.; get_*(): functions retrieve information (available licenses, R version, etc.). Visit Reference page details.  sum N.B. Users can also use functions package usethis add missing features (e.g. data/ package release tools).","code":"## Define ONCE FOR ALL your credentials ----  rcompendium::set_credentials(given = \"John\", family = \"Doe\",                               email = \"john.doe@domain.com\",                               orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")   ## CREATE A NEW EMPTY RSTUDIO PROJECT ----   ## Create an R package structure ----  rcompendium::new_package()   ## Then...  ## ... edit metadata in DESCRIPTION, CITATION, README.Rmd, etc. ## ... implement and document R functions in R/   ## Update functions documentation and NAMESPACE ----  devtools::document()   ## Update list of dependencies in DESCRIPTION ----  rcompendium::add_dependencies()   ## Check package ----  devtools::check()   ## Example: use of an add_*() function ... ## ... update 'Number of Dependencies Badge' in README.Rmd ----  rcompendium::add_dependencies_badge()"},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"resources","dir":"Articles","previous_headings":"","what":"Resources","title":"Get started with rcompendium","text":"Developing R package Working compendium","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"contributing","dir":"Articles","previous_headings":"","what":"Contributing","title":"Get started with rcompendium","text":"welcome contribute rcompendium project. Please read Contribution Guidelines. Please note rcompendium project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/rcompendium.html","id":"colophon","dir":"Articles","previous_headings":"","what":"Colophon","title":"Get started with rcompendium","text":"package result intense discussions feedback training course Data Toolbox Reproducible Research Computational Ecology. rcompendium largely inspired package rrtools developed Ben Marwick et al. tries respect standard defined community. Special thanks developers!","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"compendium-content","dir":"Articles","previous_headings":"","what":"Compendium content","title":"Working with a Compendium","text":"First, create new empty RStudio project. Let’s called comp. create new compendium structure, run rcompendium::new_compendium(). default, following content created:  create_repo = TRUE (default), new GitHub repository created directly R. available : https://github.com/{{account}}/comp/ ({{account}} either GitHub account GitHub organization). repository can private private = TRUE.","code":"comp/                             # Root of the compendium │ ├── comp.Rproj                    # RStudio project (created by user, optional) │ ├── .git/                         # GIT tracking folder ├── .gitignore                    # List of files/folders to be ignored by GIT |                                 # (specific to R language) │ ├── R/                            # R functions location │   ├── fun-demo.R                # Example of an R function (to remove) │   └── comp-package.R            # Dummy R file for high-level documentation │ ├── man/                          # R functions helps (automatically updated) │   ├── print_msg.Rd              # Documentation of the demo R function │   └── pkg-package.Rd            # High-level documentation │ ├── DESCRIPTION                   # Project metadata                              [*] ├── LICENSE.md                    # Content of the GPL (>= 2) license (default) ├── NAMESPACE                     # Automatically generated ├── .Rbuildignore                 # List of files/folders to be ignored while  │                                 # checking/installing the package │ ├── README.md                     # GitHub README (automatically generated) ├── README.Rmd                    # GitHub README                                 [*] │ ├── data/                         # User raw data (.csv, .gpkg, etc.) │   ├── raw-data/                 # Read-only files │   └── derived-data/             # Modified data derived from raw data │ ├── analyses/                     # R scripts (not function) to run analyses │ ├── outputs/                      # Outputs (R objects, .csv, etc.) ├── figures/                      # Figures (.png, .pdf, etc.) │ └── make.R                        # Main R script to source all R scripts                                    # stored in analyses/  [*] These files are automatically created but user needs to manually add      some information."},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"description","dir":"Articles","previous_headings":"Compendium metadata","what":"DESCRIPTION","title":"Working with a Compendium","text":"DESCRIPTION file contains important compendium metadata. default rcompendium creates following file: DESCRIPTION file specific R package can used work research compendia (see ). information edit file, please read https://r-pkgs.org/description.html.","code":"Package: comp Type: Package Title: The Title of the Project                                              [*] Version: 0.0.0.9000 Authors@R: c(     person(given   = \"John\",            family  = \"Doe\",            role    = c(\"aut\", \"cre\", \"cph\"),            email   = \"john.doe@domain.com\",            comment = c(ORCID = \"9999-9999-9999-9999\"))) Description: A paragraph providing a full description of the project (on     [*]      several lines...) URL: https://github.com/jdoe/comp BugReports: https://github.com/jdoe/comp/issues License: GPL (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 Imports:      devtools,     here  [*] Title and Description must be adapted by user."},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"readme","dir":"Articles","previous_headings":"Compendium metadata","what":"README","title":"Working with a Compendium","text":"README.md homepage repository GitHub. purpose help visitor understand project. Always edit README.Rmd (.md version). information, please read https://r-pkgs.org/release.html?q=README#readme.","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"recommendations","dir":"Articles","previous_headings":"","what":"Recommendations","title":"Working with a Compendium","text":"Keep root project clean possible Store raw data data/raw-data/ Document raw data modifications (R scripts /R functions) Export modified raw data data/derived-data/ (outputs/) Store R functions R/ Store R scripts /Rmd analyses/ Control project make.R file (add lines source R scripts) Built relative paths using ::() Call external functions package::function() Alternatively add #' @import package (#' @importFrom package function) R/comp-package.R call external functions function() Use devtools::document() update NAMESPACE Use rcompendium::add_dependencies(\".\") update list required dependencies DESCRIPTION use install.packages() remotes::install_deps() (install required dependencies listed DESCRIPTION) use library() devtools::load_all() (load required dependencies listed DESCRIPTION R functions stored R/) source functions use instead devtools::load_all() document everything!","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"using-renv","dir":"Articles","previous_headings":"Advanced features","what":"Using renv","title":"Working with a Compendium","text":"default structure created rcompendium::new_compendium() good starting point making analyses reproducible. can increase reproducibility using package renv. renv freeze exact package versions depend (renv.lock). ensures collaborator (future) use exact versions packages. Moreover renv provides project private package library making project isolated others. initialize renv compendium, use renv = TRUE rcompendium::new_compendium() call function rcompendium::add_renv() rcompendium::new_compendium(). make.R also updated (replacement remotes::install_deps() renv::restore())  Working renv Work usual Update NAMESPACE devtools::document() Update required dependencies DESCRIPTION rcompendium::add_dependencies(\".\") Install required dependencies locally renv::install() Save local environment renv::snapshot()","code":""},{"path":"https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","id":"using-docker","dir":"Articles","previous_headings":"Advanced features","what":"Using docker","title":"Working with a Compendium","text":"Docker tool creates self-contained environment (containers) within operating system, system libraries software (.e. R, RStudio server) frozen ready--use. use container requires recipe (Dockerfile) describes steps needed create environment. recipe, Docker image built: template container created. information Docker R users: https://environments.rstudio.com/docker add Dockerfile compendium, use dockerfile = TRUE rcompendium::new_compendium() call function rcompendium::add_dockerfile() rcompendium::new_compendium(). default rcompendium creates following Dockerfile:  use renv Docker (recommended) last step look like:  default Docker image based rocker/rstudio. can customize Dockerfile (e.g. adding system dependencies) use different default Docker image (.e. tidyverse, verse, geospatial, etc.). information: https://github.com/rocker-org/rocker-versioned2 versions R renv (applicable) specified Dockerfile local system. image built, whole project added image. container launched default working directory root project.  project ready shared, collaborator () must follow steps: Clone repository Build Docker image (terminal) Dockerfile running: docker build -t \"image_name\" . (can take time) Start container (terminal) new Docker image image_name running: docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true image_name Open Web browser visit 127.0.0.1:8787: new instance RStudio Server available everything ready--use (data, code, packages, etc.) reproduce analysis, run: source(\"make.R\")","code":"FROM rocker/rstudio:4.1.3  MAINTAINER John Doe <john.doe@domain.com>   ## Install system dependencies (for devtools) ----  RUN sudo apt update -yq \\  && sudo apt install --no-install-recommends libxml2-dev -yq \\  && sudo apt clean all \\  && sudo apt purge \\  && sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*   ## Copy local project ----  ENV folder=\"/home/rstudio/\"  COPY . $folder RUN chown -R rstudio:rstudio $folder   ## Set working directory ----  WORKDIR $folder   ## Install R packages ----  RUN R -e \"install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))\" \\  && R -e \"remotes::install_deps(upgrade = 'never')\" ## Install R packages ----  ENV RENV_VERSION 0.15.4  RUN R -e \"install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))\" \\  && R -e \"remotes::install_github('rstudio/renv@${RENV_VERSION}')\" \\  && sudo -u rstudio R -e \"renv::restore()\""},{"path":"https://frbcesab.github.io/rcompendium/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Nicolas Casajus. Author, maintainer, copyright holder.","code":""},{"path":"https://frbcesab.github.io/rcompendium/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Casajus N. (2023). rcompendium: R package create package research compendium structure. R package version 1.3, https://github.com/FRBCesab/rcompendium.","code":"@Manual{,   title = {{rcompendium}: {An} {R} package to create a package or research compendium structure},   author = {{Casajus N.}},   year = {2023},   note = {R package version 1.3},   url = {https://github.com/FRBCesab/rcompendium}, }"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"rcompendium-","dir":"","previous_headings":"","what":"Create a Package or Research Compendium Structure","title":"Create a Package or Research Compendium Structure","text":"area open science, making reproducible analyses strong prerequisite. sometimes difficult 1) find good structure organize files 2) set whole project. aim package rcompendium make easier creation R package/research compendium (.e. predefined files/folders structure) users can focus code/analysis instead wasting time organizing files. full ready--work structure set following features: Initialization version control git. Creation minimal R package structure (DESCRIPTION NAMESPACE files, R/ man/ folders). Creation additional files (LICENSE.md, inst/CITATION, etc.). Creation Get started vignette vignettes/ (package ). Setting units tests process tests/. Creation README.Rmd HexSticker (template) badges. Autocompletion maintainer information. Initialization renv system (required). Creation Dockerfile (required). Creation GitHub repository. check test package (R CMD Check); report code coverage (covr); build deploy website (pkgdown); render README.md. package heavily relies R packages devtools usethis follows recommendations made Hadley Wickham & Jenny Bryan Ben Marwick.","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create a Package or Research Compendium Structure","text":"can install stable version CRAN : can install development version GitHub : Note: Unix system may error installation linked V8 JavaScript engine. software required R package cffr (included rcompendium). Run following line try reinstall rcompendium.","code":"## Install stable version of < rcompendium > from CRAN ---- install.packages(\"rcompendium\") ## Install < remotes > package (if not already installed) ---- if (!requireNamespace(\"remotes\", quietly = TRUE)) {   install.packages(\"remotes\") }  ## Install dev version of < rcompendium > from GitHub ---- remotes::install_github(\"FRBCesab/rcompendium\") ## Fix V8 issues ---- Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)  ## Install < rcompendium > ---- install.packages(\"rcompendium\")"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create a Package or Research Compendium Structure","text":"Please read Get started vignette pay attention sections Prerequisites Usage Others available vignettes: Developing Package Working Compendium","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Create a Package or Research Compendium Structure","text":"Please cite package : Casajus N. (2023) rcompendium: R package create package research compendium structure. Version 1.3, https://github.com/FRBCesab/rcompendium. can also run:","code":"citation(\"rcompendium\")  ## A BibTeX entry for LaTeX users is: ##  ## @Manual{, ##   title  = {{rcompendium}: {An} {R} package to create a package or research compendium structure}, ##   author = {{Casajus N.}}, ##   year   = {2023}, ##   note   = {R package version 1.3}, ##   url    = {https://github.com/FRBCesab/rcompendium}, ## }"},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Create a Package or Research Compendium Structure","text":"types contributions encouraged valued. information, check Contribution Guidelines. Please note rcompendium project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://frbcesab.github.io/rcompendium/index.html","id":"colophon","dir":"","previous_headings":"","what":"Colophon","title":"Create a Package or Research Compendium Structure","text":"package result intense discussions feedbacks training course Reproducible Research Computational Ecology. rcompendium largely inspired package rrtools developed Ben Marwick et al. tries respect standard defined community.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a CITATION file — add_citation","title":"Create a CITATION file — add_citation","text":"function creates CITATION file folder inst/. file contains BiBTeX entry cite package manual. User need edit hand information (title, version, etc.).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a CITATION file — add_citation","text":"","code":"add_citation(   given = NULL,   family = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a CITATION file — add_citation","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a CITATION file — add_citation","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a CITATION file — add_citation","text":"","code":"if (FALSE) { add_citation() readCitationFile(\"inst/CITATION\") citation(\"pkg\")    # If you have installed your package <pkg> }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":null,"dir":"Reference","previous_headings":"","what":"Add code of conduct — add_code_of_conduct","title":"Add code of conduct — add_code_of_conduct","text":"function creates CODE_OF_CONDUCT.md file adapted Contributor Covenant, version 2.1 available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add code of conduct — add_code_of_conduct","text":"","code":"add_code_of_conduct(   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add code of conduct — add_code_of_conduct","text":"email character length 1. email address project maintainer. open logical value. TRUE (default) CONTRIBUTING.md file opened editor. overwrite logical value. files already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add code of conduct — add_code_of_conduct","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_code_of_conduct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add code of conduct — add_code_of_conduct","text":"","code":"if (FALSE) { add_code_of_conduct() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Codecov badge — add_codecov_badge","title":"Add a Codecov badge — add_codecov_badge","text":"function adds Code coverage badge README.Rmd, .e. percentage code cover units tests. percentage computed codecov.io service. Note: service must manually activated package visiting https://.codecov.io/. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Codecov badge — add_codecov_badge","text":"","code":"add_codecov_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Codecov badge — add_codecov_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Codecov badge — add_codecov_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_codecov_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Codecov badge — add_codecov_badge","text":"","code":"if (FALSE) { add_codecov_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":null,"dir":"Reference","previous_headings":"","what":"Create additional folders — add_compendium","title":"Create additional folders — add_compendium","text":"function creates compendium, .e. additional folders package structure. default, following directories created: data/raw-data, data/derived-data, analyses/, outputs/, figures/. README.md added folder must edited. argument compendium allows user choose compendium structure. theses folders added .Rbuildignore file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create additional folders — add_compendium","text":"","code":"add_compendium(compendium = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create additional folders — add_compendium","text":"compendium character vector specifying folders created. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create additional folders — add_compendium","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_compendium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create additional folders — add_compendium","text":"","code":"if (FALSE) { add_compendium() add_compendium(compendium = \"paper\") add_compendium(compendium = c(\"data\", \"outputs\", \"code\", \"manuscript\")) }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":null,"dir":"Reference","previous_headings":"","what":"Add contribution guidelines — add_contributing","title":"Add contribution guidelines — add_contributing","text":"function creates several files help user learn contribute project: CONTRIBUTING.md: general guidelines outlining best way contribute project (can modified); .github/ISSUE_TEMPLATE/bug_report.md: issue template report bug (can modified); .github/ISSUE_TEMPLATE/feature_request.md: issue template suggest new feature (can modified); .github/ISSUE_TEMPLATE/other_issue.md: issue template types issue (can modified).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add contribution guidelines — add_contributing","text":"","code":"add_contributing(   email = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add contribution guidelines — add_contributing","text":"email character length 1. email address project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) CONTRIBUTING.md file opened editor. overwrite logical value. files already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add contribution guidelines — add_contributing","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_contributing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add contribution guidelines — add_contributing","text":"","code":"if (FALSE) { add_contributing() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a CRAN Status badge — add_cran_badge","title":"Add a CRAN Status badge — add_cran_badge","text":"function adds CRAN Status badge README.Rmd. package hosted CRAN badge indicate published CRAN. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a CRAN Status badge — add_cran_badge","text":"","code":"add_cran_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a CRAN Status badge — add_cran_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a CRAN Status badge — add_cran_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_cran_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a CRAN Status badge — add_cran_badge","text":"","code":"if (FALSE) { add_cran_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Add dependencies in DESCRIPTION — add_dependencies","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"function detects external dependencies used R/, NAMESPACE, @examples sections roxygen2 headers automatically adds dependencies Imports section DESCRIPTION file. NAMESPACE function detects dependencies mentioned import(pkg) importFrom(pkg,fun). R/ folder detects functions called pkg::fun() code R files. @examples sections also detects packages attached library() require(). vignettes/ folder also inspected detected dependencies (pkg::fun(), library() require()) added Suggests field DESCRIPTION file (addition packages knitr rmarkdown). project research compendium user can also inspect additional folder(s) argument compendium add dependencies Imports section DESCRIPTION file. detection process one used vignettes/. tests/ folder also inspected detected dependencies (pkg::fun(), library() require()) added Suggests field DESCRIPTION file (addition package testthat).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"","code":"add_dependencies(compendium = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"compendium character length 1. name folder recursively detect dependencies added Imports field DESCRIPTION file. can 'analysis/' (additional folders, .e. data/, outputs/, figures/, etc. created folder), '.' (folders data/, outputs/, figures/, etc. created root project), etc. See new_compendium() information. Default compendium = NULL (.e. additional folder inspected R/, NAMESPACE, vignettes/, tests/ still inspected).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add dependencies in DESCRIPTION — add_dependencies","text":"","code":"if (FALSE) { add_dependencies() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Dependencies badge — add_dependencies_badge","title":"Add a Dependencies badge — add_dependencies_badge","text":"function adds updates Dependencies badge README.Rmd. first number corresponds direct dependencies second recursive dependencies. Note: function can work packages published CRAN based function gtools::getDependencies(). See also function get_all_dependencies(). Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Dependencies badge — add_dependencies_badge","text":"","code":"add_dependencies_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Dependencies badge — add_dependencies_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Dependencies badge — add_dependencies_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dependencies_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Dependencies badge — add_dependencies_badge","text":"","code":"if (FALSE) { add_dependencies_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a DESCRIPTION file — add_description","title":"Create a DESCRIPTION file — add_description","text":"function creates DESCRIPTION file root project. file contains metadata project. information (title, description, version, etc.) must edited hand. information: https://r-pkgs.org/description.html. User credentials can passed arguments recommended store .Rprofile file set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a DESCRIPTION file — add_description","text":"","code":"add_description(   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a DESCRIPTION file — add_description","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. orcid character length 1. ORCID project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. open logical value. TRUE (default) file opened editor. overwrite logical value. DESCRIPTION already present overwrite = TRUE, file erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a DESCRIPTION file — add_description","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_description.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a DESCRIPTION file — add_description","text":"","code":"if (FALSE) { add_description(organisation = \"MySociety\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Dockerfile — add_dockerfile","title":"Create a Dockerfile — add_dockerfile","text":"function creates Dockerfile root project based template. Docker image based rocker/rstudio. whole project copied image R packages installed (using renv::restore() remotes::install_deps()). addition .dockerignore file added ignore files/folders building image. User can customize Dockerfile (e.g. system dependencies). /can also use different default Docker image (.e. tidyverse, verse, geospatial, etc.). information: https://github.com/rocker-org/rocker-versioned2 default versions R renv (applicable) specified Dockerfile local system. project ready released, user must build Docker image running: docker build -t \"image_name\" . run container, user must run: docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true image_name new instance RStudio Server available Web browser URL: 127.0.0.1:8787.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Dockerfile — add_dockerfile","text":"","code":"add_dockerfile(   given = NULL,   family = NULL,   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Dockerfile — add_dockerfile","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. open logical value. TRUE (default) Dockerfile opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Dockerfile — add_dockerfile","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_dockerfile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a Dockerfile — add_dockerfile","text":"","code":"if (FALSE) { add_dockerfile() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to check package — add_github_actions_check","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"function creates configuration file (.yaml) setup GitHub Actions check package. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/R-CMD-check.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"","code":"add_github_actions_check(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"return value.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"workflow runs R CMD check three major operating systems (Ubuntu, macOS, Windows) using latest release R. package also checked Ubuntu (latest version) using development previous versions R.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to check package — add_github_actions_check","text":"","code":"if (FALSE) { add_github_actions_check() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a R CMD Check badge — add_github_actions_check_badge","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"function adds R CMD Check badge README.Rmd. function must run add_github_actions_check() setup GitHub Actions check test package. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"","code":"add_github_actions_check_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_check_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a R CMD Check badge — add_github_actions_check_badge","text":"","code":"if (FALSE) { add_github_actions_check_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"function creates configuration file (.yaml) setup GitHub Actions update CITATION.cff. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/update-citation-cff.yaml. function also create CITATION.cff using package cffr.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"","code":"add_github_actions_citation(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_citation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to update CITATION.cff — add_github_actions_citation","text":"","code":"if (FALSE) { add_github_actions_citation() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"function creates configuration file (.yaml) setup GitHub Actions report code coverage testing package. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/test-coverage.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"","code":"add_github_actions_codecov(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to report code coverage — add_github_actions_codecov","text":"","code":"if (FALSE) { add_github_actions_codecov() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Test coverage badge — add_github_actions_codecov_badge","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"function adds Test coverage badge README.Rmd. function must run add_github_actions_codecov() setup GitHub Actions report percentage code cover units tests. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"","code":"add_github_actions_codecov_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_codecov_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Test coverage badge — add_github_actions_codecov_badge","text":"","code":"if (FALSE) { add_github_actions_codecov_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to document package — add_github_actions_document","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"function creates configuration file (.yaml) setup GitHub Actions document package update Rd files man/, NAMESPACE DESCRIPTION files. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/document-package.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"","code":"add_github_actions_document(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_document.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to document package — add_github_actions_document","text":"","code":"if (FALSE) { add_github_actions_document() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"function creates configuration file (.yaml) setup GitHub Actions automatically build deploy website using pkgdown. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/pkgdown.yaml. additional empty file (_pkgdown.yaml) also written: can used customize website.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"","code":"add_github_actions_pkgdown(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to build and deploy package website — add_github_actions_pkgdown","text":"","code":"if (FALSE) { add_github_actions_pkgdown() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Website badge — add_github_actions_pkgdown_badge","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"function adds Website badge README.Rmd. function must run add_github_actions_pkgdown() setup GitHub Actions build deploy package website. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"","code":"add_github_actions_pkgdown_badge(organisation = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_pkgdown_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Website badge — add_github_actions_pkgdown_badge","text":"","code":"if (FALSE) { add_github_actions_pkgdown_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup GitHub Actions to render README — add_github_actions_render","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"function creates configuration file (.yaml) setup GitHub Actions automatically knit README.Rmd push. workflow triggered README.Rmd modified since last commit. workflow derived https://github.com/r-lib/actions/tree/v2-branch/examples. file written .github/workflows/render-README.yaml.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"","code":"add_github_actions_render(open = FALSE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_github_actions_render.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setup GitHub Actions to render README — add_github_actions_render","text":"","code":"if (FALSE) { add_github_actions_render() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a LICENSE — add_license","title":"Add a LICENSE — add_license","text":"function adds license project. add license name License field DESCRIPTION file write content license License.md file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a LICENSE — add_license","text":"","code":"add_license(license = NULL, given = NULL, family = NULL, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a LICENSE — add_license","text":"license character length 1. chosen license. Run get_licenses()) select appropriate one. given character length 1. given name copyright holder. required license = 'MIT'. NULL (default) license = 'MIT', function try retrieve value parameter .Rprofile file (edited set_credentials()). family character length 1. family name copyright holder. required license = 'MIT'. NULL (default) license = 'MIT', function try retrieve value parameter .Rprofile file (edited set_credentials()). quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a LICENSE — add_license","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a LICENSE — add_license","text":"","code":"if (FALSE) { add_license(license = \"MIT\") add_license(license = \"GPL (>= 2)\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a License badge — add_license_badge","title":"Add a License badge — add_license_badge","text":"function adds updates License badge README.Rmd. function reads License field DESCRIPTION file. Ensure field correctly defined. See add_license() detail. function requires presence DESCRIPTION file project root. See add_description() detail. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a License badge — add_license_badge","text":"","code":"add_license_badge(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a License badge — add_license_badge","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a License badge — add_license_badge","text":"badge markdown expression.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_license_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a License badge — add_license_badge","text":"","code":"if (FALSE) { add_license_badge() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Life Cycle badge — add_lifecycle_badge","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"function adds updates Life Cycle badge README.Rmd. based standard defined https://lifecycle.r-lib.org/articles/stages.html. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"","code":"add_lifecycle_badge(lifecycle = \"experimental\", quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"lifecycle character length 1. Accepted stages : 'experimental' (default), 'stable', 'deprecated', 'superseded'. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"badge markdown expression.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"project can following life cycle stage: Experimental - experimental project made available user can try provide feedback, come promises long term stability. Stable - project considered stable author happy interface, see major issues, happy share world. Superseded - superseded project known better alternative, going away. Superseded project receive new features, receive critical bug fixes needed keep working. Deprecated - deprecated project better alternative available scheduled removal.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_lifecycle_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Life Cycle badge — add_lifecycle_badge","text":"","code":"if (FALSE) { add_lifecycle_badge() add_lifecycle_badge(lifecycle = \"stable\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Make-like R file — add_makefile","title":"Create a Make-like R file — add_makefile","text":"function creates Make-like R file (make.R) root project based template. used project research compendium. content file provides guidelines. See also new_compendium() information.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Make-like R file — add_makefile","text":"","code":"add_makefile(   given = NULL,   family = NULL,   email = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Make-like R file — add_makefile","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Make-like R file — add_makefile","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_makefile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a Make-like R file — add_makefile","text":"","code":"if (FALSE) { add_makefile() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a package-level documentation file — add_package_doc","title":"Create a package-level documentation file — add_package_doc","text":"function adds package-level documentation file (pkg-package.R) R/ folder. file make help available user via ?pkg (pkg name package). good place put general directives like @import @importFrom.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a package-level documentation file — add_package_doc","text":"","code":"add_package_doc(open = TRUE, overwrite = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a package-level documentation file — add_package_doc","text":"open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a package-level documentation file — add_package_doc","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_package_doc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a package-level documentation file — add_package_doc","text":"","code":"if (FALSE) { add_package_doc() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":null,"dir":"Reference","previous_headings":"","what":"Add minimal R version to DESCRIPTION — add_r_depend","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"function adds minimal R version Depends field DESCRIPTION file. version corresponds higher version R among dependencies. dependencies mentions minimal R version, DESCRIPTION modified.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"","code":"add_r_depend()"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_r_depend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add minimal R version to DESCRIPTION — add_r_depend","text":"","code":"if (FALSE) { add_r_depend() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a README file — add_readme_rmd","title":"Create a README file — add_readme_rmd","text":"function creates README.Rmd file root project based template. edited user needs knit README.md (use function refresh()).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a README file — add_readme_rmd","text":"","code":"add_readme_rmd(   type = \"package\",   given = NULL,   family = NULL,   organisation = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a README file — add_readme_rmd","text":"type character length 1. package (default) GitHub README.Rmd specific R package created. compendium GitHub README.Rmd specific research compendium created. given character length 1. given name project maintainer. family character length 1. family name project maintainer. organisation character length 1. name GitHub organisation host package. NULL (default) GitHub account used. argument used set URL package (hosted GitHub). open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a README file — add_readme_rmd","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_readme_rmd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a README file — add_readme_rmd","text":"","code":"if (FALSE) { add_readme_rmd(type = \"package\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize renv — add_renv","title":"Initialize renv — add_renv","text":"function initializes renv environment project running renv::init(). See https://rstudio.github.io/renv/ detail.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize renv — add_renv","text":"","code":"add_renv(quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize renv — add_renv","text":"quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize renv — add_renv","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize renv — add_renv","text":"","code":"if (FALSE) { add_renv() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Repository Status badge — add_repostatus_badge","title":"Add a Repository Status badge — add_repostatus_badge","text":"function adds updates Repository Status badge project README.Rmd. based standard defined https://www.repostatus.org project. Make sure 1) README.Rmd file exists project root 2) contains block starting line <!-- badges: start --> ending line <!-- badges: end -->. forget re-render README.md.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Repository Status badge — add_repostatus_badge","text":"","code":"add_repostatus_badge(status = \"concept\", quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Repository Status badge — add_repostatus_badge","text":"status character length 1. Accepted status : 'concept' (default), 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Repository Status badge — add_repostatus_badge","text":"badge markdown expression.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a Repository Status badge — add_repostatus_badge","text":"project can following status: Concept - Minimal implementation done yet, repository intended limited example, demo, proof--concept. WIP - Initial development progress, yet stable, usable release suitable public. Suspended - Initial development started, yet stable, usable release; work stopped time author(s) intend resuming work. Abandoned - Initial development started, yet stable, usable release; project abandoned author(s) intend continuing development. Active - project reached stable, usable state actively developed. Inactive - project reached stable, usable state longer actively developed; support/maintenance provided time allows. Unsupported - project reached stable, usable state author(s) ceased work . new maintainer may desired.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_repostatus_badge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Repository Status badge — add_repostatus_badge","text":"","code":"if (FALSE) { add_repostatus_badge() add_repostatus_badge(status = \"active\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize units tests — add_testthat","title":"Initialize units tests — add_testthat","text":"function initializes units tests settings running usethis::use_testthat() adding example units tests file tests/testthat/test-demo.R. sample file test demo function created R/fun-demo.R.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize units tests — add_testthat","text":"","code":"add_testthat()"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize units tests — add_testthat","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_testthat.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize units tests — add_testthat","text":"","code":"if (FALSE) { add_testthat() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to the .Rbuildignore file — add_to_buildignore","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"function adds files/folders .Rbuildignore file. .Rbuildignore already present, files ignored checking package just added file. Otherwise new file created.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"","code":"add_to_buildignore(x, open = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"x character vector. One several files/folders names added .Rbuildignore. argument mandatory. open logical value. TRUE .Rbuildignore file opened editor. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_buildignore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add to the .Rbuildignore file — add_to_buildignore","text":"","code":"if (FALSE) { add_to_buildignore(open = TRUE) add_to_buildignore(\".DS_Store\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Add to the .gitignore file — add_to_gitignore","title":"Add to the .gitignore file — add_to_gitignore","text":"function creates .gitignore file root project based template (specific R). .gitignore already present, files untracked git just added file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add to the .gitignore file — add_to_gitignore","text":"","code":"add_to_gitignore(x, open = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add to the .gitignore file — add_to_gitignore","text":"x character vector. One several files/folders names added .gitignore. open logical value. TRUE .gitignore file opened editor. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add to the .gitignore file — add_to_gitignore","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_to_gitignore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add to the .gitignore file — add_to_gitignore","text":"","code":"if (FALSE) { add_to_gitignore(open = TRUE) add_to_gitignore(\".DS_Store\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a vignette document — add_vignette","title":"Create a vignette document — add_vignette","text":"function adds vignette folder vignettes/. also adds dependencies knitr rmarkdown field Suggests DESCRIPTION file (already present fields Imports).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a vignette document — add_vignette","text":"","code":"add_vignette(   filename = NULL,   title = NULL,   open = TRUE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a vignette document — add_vignette","text":"filename character length 1. name .Rmd file created. NULL (default ) .Rmd file named pkg.Rmd pkg package name. title character length 1. title vignette. NULL (default) title Get started. open logical value. TRUE (default) file opened editor. overwrite logical value. file already present overwrite = TRUE, erased replaced. Default FALSE. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a vignette document — add_vignette","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/add_vignette.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a vignette document — add_vignette","text":"","code":"if (FALSE) { ## Default vignette ---- add_vignette()  ## Default vignette ---- add_vignette(filename = \"pkg\", title = \"Get started\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Get all external dependencies — get_all_dependencies","title":"Get all external dependencies — get_all_dependencies","text":"function gets external packages project needs. used generate Dependencies badge (add_dependencies_badge()).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get all external dependencies — get_all_dependencies","text":"","code":"get_all_dependencies(pkg = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get all external dependencies — get_all_dependencies","text":"pkg character length 1. name CRAN package NULL (default). NULL get dependencies local (uninstalled) project (package compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get all external dependencies — get_all_dependencies","text":"list three vectors: base_deps, vector base packages; direct_deps, vector direct packages; all_deps, vector dependencies (recursively obtained).","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_dependencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get all external dependencies — get_all_dependencies","text":"","code":"if (FALSE) { ## Update dependencies ---- add_dependencies()  ## Get all dependencies ---- deps <- get_all_dependencies() unlist(lapply(deps, length))  ## Can be used for a CRAN package ---- deps <- get_all_dependencies(\"usethis\") unlist(lapply(deps, length)) }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"List all functions in the package — get_all_functions","title":"List all functions in the package — get_all_functions","text":"function returns list functions (exported internal) available package. function scans NAMESPACE R/ folder, recommended run devtools::document() .","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all functions in the package — get_all_functions","text":"","code":"get_all_functions()"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all functions in the package — get_all_functions","text":"list two vectors: external, vector exported functions name; internal, vector internal functions name.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_all_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all functions in the package — get_all_functions","text":"","code":"if (FALSE) { ## Update NAMESPACE ---- devtools::document()  ## List all implemented functions ---- get_all_functions() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":null,"dir":"Reference","previous_headings":"","what":"List all available licenses — get_licenses","title":"List all available licenses — get_licenses","text":"function returns list available licenses. particularly useful get right spelling license passed new_package(), new_compendium(), add_license().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all available licenses — get_licenses","text":"","code":"get_licenses()"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all available licenses — get_licenses","text":"data.frame following two variables: tag, license name used add_license(); url, URL license description.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_licenses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all available licenses — get_licenses","text":"","code":"get_licenses() #>                      tag                                             url #> 1                    MIT        https://choosealicense.com/licenses/mit/ #> 2                    CC0    https://choosealicense.com/licenses/cc0-1.0/ #> 3              CC BY 4.0  https://choosealicense.com/licenses/cc-by-4.0/ #> 4                  GPL-2    https://choosealicense.com/licenses/gpl-2.0/ #> 5                  GPL-3    https://choosealicense.com/licenses/gpl-3.0/ #> 6             GPL (>= 2)    https://choosealicense.com/licenses/gpl-2.0/ #> 7             GPL (>= 3)    https://choosealicense.com/licenses/gpl-3.0/ #> 8               LGPL-2.1   https://choosealicense.com/licenses/lgpl-2.1/ #> 9                 LGPL-3   https://choosealicense.com/licenses/lgpl-3.0/ #> 10         LGPL (>= 2.1)   https://choosealicense.com/licenses/lgpl-2.1/ #> 11           LGPL (>= 3)   https://choosealicense.com/licenses/lgpl-3.0/ #> 12                AGPL-3   https://choosealicense.com/licenses/agpl-3.0/ #> 13           AGPL (>= 3)   https://choosealicense.com/licenses/agpl-3.0/ #> 14 Apache License (== 2) https://choosealicense.com/licenses/apache-2.0/ #> 15 Apache License (>= 2) https://choosealicense.com/licenses/apache-2.0/"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get required minimal R version — get_minimal_r_version","title":"Get required minimal R version — get_minimal_r_version","text":"function detects minimal required R version project based minimal required R version dependencies. can used update Depends field DESCRIPTION file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get required minimal R version — get_minimal_r_version","text":"","code":"get_minimal_r_version(pkg = NULL)"},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get required minimal R version — get_minimal_r_version","text":"pkg character length 1. name CRAN package NULL (default). NULL get minimal required R version local (uninstalled) project (package compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get required minimal R version — get_minimal_r_version","text":"character minimal required R version.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/get_minimal_r_version.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get required minimal R version — get_minimal_r_version","text":"","code":"if (FALSE) { ## Update dependencies ---- add_dependencies()  ## Minimal R version of a project ---- get_minimal_r_version()  ## Minimal R version of a CRAN package ---- get_minimal_r_version(\"usethis\") }"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an R compendium structure — new_compendium","title":"Create an R compendium structure — new_compendium","text":"function creates research compendium (.e. predefined files/folders structure) help user organizing files/folders run analysis. addition common R packages files/folders (see new_package() information) function created following folders: data/: folder store raw data. Note data must never modified. user want modify recommended export new data outputs/. analyses/: folder write analyses instructions, .e. R scripts. user need create R functions recommended write R/ folder. outputs/: folder store intermediate final outputs generated R scripts. figures/: folder store figures generated R scripts. function also creates Make-like R file (make.R). file contains two main lines: devtools::install_deps(): downloads external dependencies required project (alternative install.packages()). Ideal sharing; devtools::load_all(): loads external dependencies R functions (alternative library() source() respectively). user writes R scripts /can add following line file: source(::(\"rscripts\", \"script_X.R\")). /can source entire make.R run analysis. function add_dependencies() can used automatically add external dependencies DESCRIPTION file. recommended, better reproducibility, call external dependencies pkg::fun() @import @importFrom R functions instead using library(). files/folders added .Rbuildignore rest project (e.g. R functions) can used (installed) R package.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an R compendium structure — new_compendium","text":"","code":"new_compendium(   compendium = NULL,   license = \"GPL (>= 2)\",   status = NULL,   lifecycle = NULL,   contributing = TRUE,   code_of_conduct = TRUE,   vignette = FALSE,   test = FALSE,   create_repo = TRUE,   private = FALSE,   gh_check = FALSE,   codecov = FALSE,   website = FALSE,   gh_render = FALSE,   gh_citation = FALSE,   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   renv = FALSE,   dockerfile = FALSE,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an R compendium structure — new_compendium","text":"compendium character vector specifying folders created. See add_compendium() information. license character vector length 1. license used project. Run get_licenses() choose appropriate one. Default license = 'GPL (>= 2)' license can changed later calling add_license() (add_license_badge() refresh() update corresponding badge README). status character vector length 1. status project according standard defined https://www.repostatus.org project. One among 'concept', 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. See add_repostatus_badge() information. argument used add badge README.Rmd help visitors better understand project. Default status = NULL. status can added/changed later using add_repostatus_badge(). lifecycle character vector length 1. life cycle stage project according standard defined https://lifecycle.r-lib.org/articles/stages.html. One among 'experimental', 'stable', 'deprecated', 'superseded'. See add_lifecycle_badge() information. argument used add badge README.Rmd help visitors better understand project. Default lifecycle = NULL. stage can added/changed later using add_lifecycle_badge(). contributing logical value. TRUE (default) adds CONTRIBUTING.md file ISSUE_TEMPLATES. See add_contributing() information. code_of_conduct logical value. TRUE (default) adds CODE_OF_CONDUCT.md file. See add_code_of_conduct() information. vignette logical value. TRUE creates vignette vignettes/. Packages knitr rmarkdown also added Suggests field DESCRIPTION file. Default FALSE. test logical value. TRUE initializes units tests running usethis::use_testthat(). Package testthat also added Suggests field DESCRIPTION file. Default FALSE. create_repo logical value. TRUE (default) creates repository (public private = FALSE private private = TRUE) GitHub. See section Creating GitHub repo help page new_package(). private logical value. TRUE creates private repository user GitHub account (organisation). Default private = FALSE. gh_check logical value. TRUE configures GitHub Actions automatically check test package push. run R CMD check three major operating systems (Ubuntu, macOS, Windows) latest release R. See add_github_actions_check() information. create_repo = FALSE argument ignored. Default FALSE. codecov logical value. TRUE configures GitHub Actions automatically report code coverage units tests push. See add_github_actions_codecov() information. create_repo = FALSE argument ignored. Default FALSE. website logical value. TRUE configures GitHub Actions automatically build deploy package website (using pkgdown) push. gh-pages branch created using usethis::use_github_pages() GitHub repository automatically configured deploy website. create_repo = FALSE argument ignored. Default FALSE. gh_render logical value. TRUE configures GitHub Actions automatically knit README.Rmd push. See add_github_actions_render() information. create_repo = FALSE argument ignored. Default FALSE. gh_citation logical value. TRUE configures GitHub Actions automatically update CITATION.cff file. See add_github_actions_citation() information. create_repo = FALSE argument ignored. Default FALSE. given character vector length 1. given name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). family character vector length 1. family name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). email character vector length 1. email address maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). orcid character vector length 1. ORCID maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials(). organisation character vector length 1. GitHub organisation host repository. defined overwrite GitHub pseudo. Default organisation = NULL (GitHub pseudo used). renv logical value. TRUE initializes renv environment project running renv::init(). Package renv also added Imports field DESCRIPTION file. Default FALSE. dockerfile logical value. TRUE creates Dockerfile project. See add_dockerfile() detail. Default FALSE. overwrite logical value. TRUE files written templates modified user erased. Default overwrite = FALSE. careful using argument. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an R compendium structure — new_compendium","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/new_compendium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an R compendium structure — new_compendium","text":"","code":"if (FALSE) { library(rcompendium)  ## Define **ONCE FOR ALL** your credentials ---- set_credentials(given = \"John\", family = \"Doe\",                  email = \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")  ## Create an R package ---- new_compendium()  ## Start adding data and developing functions and scripts ---- ## ...  ## Update package (documentation, dependencies, README, check) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an R package structure — new_package","title":"Create an R package structure — new_package","text":"function creates new R package structure according current best practices. Essential features R package created (DESCRIPTION NAMESPACE files, R/ man/ folders). project also versioned git generic R .gitignore added. IMPORTANT - using function user needs create new folder (new project using RStudio) run function inside folder (using setwd() opening Rproj new RStudio session). name package name folder. rules must respected: https://r-pkgs.org/workflow101.html#name--package. fields DESCRIPTION file (maintainer information, package name, license, URLs,  roxygen2 version)  automatically filled others (like title description) need edited manually. Additional features also created: CITATION file, README.Rmd, tests/ vignettes/ folders (optional). See vignette Get started complete overview full structure. GitHub repository can also created (default) following \"GitHub last\" workflow (https://happygitwithr.com/existing-github-last.html). Configuration files GitHub Actions automatically 1) check package, 2) test report code coverage, 3) deploy website using pkgdown added .github/ folder. See section Creating GitHub repo.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an R package structure — new_package","text":"","code":"new_package(   license = \"GPL (>= 2)\",   status = NULL,   lifecycle = NULL,   contributing = TRUE,   code_of_conduct = TRUE,   vignette = TRUE,   test = TRUE,   create_repo = TRUE,   private = FALSE,   gh_check = TRUE,   codecov = TRUE,   website = TRUE,   gh_render = TRUE,   gh_citation = TRUE,   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   organisation = NULL,   overwrite = FALSE,   quiet = FALSE )"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an R package structure — new_package","text":"license character vector length 1. license used package. Run get_licenses() choose appropriate one. Default license = 'GPL (>= 2)' license can changed later calling add_license() (add_license_badge() refresh() update corresponding badge README). status character vector length 1. status project according standard defined  https://www.repostatus.org project. One among 'concept', 'wip', 'suspended', 'abandoned', 'active', 'inactive', 'unsupported'. See add_repostatus_badge() information. argument used add badge README.Rmd help visitors better understand project. want badge use status = NULL (default). status can added/changed later using add_repostatus_badge(). lifecycle character vector length 1. life cycle stage project according standard defined https://lifecycle.r-lib.org/articles/stages.html. One among 'experimental', 'stable', 'deprecated', 'superseded'. See add_lifecycle_badge() information. argument used add badge README.Rmd help visitors better understand project. want badge use lifecycle = NULL (default). stage can added/changed later using add_lifecycle_badge(). contributing logical value. TRUE (default) adds CONTRIBUTING.md file ISSUE_TEMPLATES. See add_contributing() information. code_of_conduct logical value. TRUE (default) adds CODE_OF_CONDUCT.md file. See add_code_of_conduct() information. vignette logical value. TRUE (default) creates vignette vignettes/. Packages knitr rmarkdown also added Suggests field DESCRIPTION file. test logical value. TRUE (default) initializes units tests running usethis::use_testthat(). Package testthat also added Suggests field DESCRIPTION file. create_repo logical value. TRUE (default) creates repository (public private = FALSE private private = TRUE) GitHub. See section Creating GitHub repo. private logical value. TRUE creates private repository user GitHub account (organisation). Default private = FALSE. gh_check logical value. TRUE (default) configures GitHub Actions automatically check test package push. run R CMD check three major operating systems (Ubuntu, macOS, Windows) latest release R. See add_github_actions_check() information. create_repo = FALSE argument ignored. codecov logical value. TRUE (default) configures GitHub Actions automatically report code coverage units tests push. See add_github_actions_codecov() information. create_repo = FALSE argument ignored. website logical value. TRUE (default) configures GitHub Actions automatically build deploy package website (using pkgdown) push. gh-pages branch created using usethis::use_github_pages() GitHub repository automatically configured deploy website. create_repo = FALSE argument ignored. gh_render logical value. TRUE (default) configures GitHub Actions automatically knit README.Rmd push. See add_github_actions_render() information. create_repo = FALSE argument ignored. gh_citation logical value. TRUE (default) configures GitHub Actions automatically update CITATION.cff file. See add_github_actions_citation() information. create_repo = FALSE argument ignored. given character vector length 1. given name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. family character vector length 1. family name maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. email character vector length 1. email address maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. orcid character vector length 1. ORCID maintainer package. NULL (default) function try get value reading .Rprofile file. information see set_credentials() section Managing credentials. organisation character vector length 1. GitHub organisation host repository. defined overwrite GitHub pseudo. Default organisation = NULL (GitHub pseudo used). overwrite logical value. TRUE files written templates modified user erased. Default overwrite = FALSE. careful using argument. quiet logical value. TRUE messages deleted. Default FALSE.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an R package structure — new_package","text":"return value.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"recommended-workflow","dir":"Reference","previous_headings":"","what":"Recommended workflow","title":"Create an R package structure — new_package","text":"purpose package rcompendium make easier creation R package/research compendium user can focus code/analysis instead wasting time organizing files. recommended workflow : Create empty RStudio project; Store credentials set_credentials() (already done); Run new_package() create new package structure (GitHub repository); Edit metadata DESCRIPTION, CITATION, README.Rmd; Implement, document & test functions (fun part); Update project (update .Rd files, NAMESPACE, external dependencies DESCRIPTION, re-knit README.Rmd, check package integrity) refresh(); Repeat steps 5 6 developing package.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"managing-credentials","dir":"Reference","previous_headings":"","what":"Managing credentials","title":"Create an R package structure — new_package","text":"can use arguments given, family, email, orcid directly function new_package() (others). create lot projects (packages /compendiums) can frustrating long run. alternative use function set_credentials() permanently store information .Rprofile file. arguments set NULL (default) function package rcompendium search .Rprofile file. save time (purpose package). Even stored information .Rprofile file always able modify --fly (.e. using arguments new_package()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"configuring-git","dir":"Reference","previous_headings":"","what":"Configuring git","title":"Create an R package structure — new_package","text":"First run gh::gh_whoami() see git correctly configured. see something like:   Otherwise might need run:   See gert::git_config_global_set() information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name  = \"user.name\",                              value = \"John Doe\")                              gert::git_config_global_set(name  = \"user.email\",                              value = \"john.doe@domain.com\")                              gert::git_config_global_set(name  = \"github.user\",                              value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"creating-a-github-repo","dir":"Reference","previous_headings":"","what":"Creating a GitHub repo","title":"Create an R package structure — new_package","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). GITHUB PAT locally stored, must: Obtain new one GitHub account. Make sure select least first two scopes (private repository workflow) Store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9' Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured see something like calling gh::gh_whoami():   able create GitHub repository directly R!","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"delete_repo, repo, workflow\",   \"token\": \"ghp_99z9...z9\" }"},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/new_package.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an R package structure — new_package","text":"","code":"if (FALSE) { library(rcompendium)  ## Define **ONCE FOR ALL** your credentials ---- set_credentials(given = \"John\", family = \"Doe\",                  email = \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"ssh\")  ## Create an R package ---- new_package()  ## Start developing functions ---- ## ...  ## Update package (documentation, dependencies, README, check) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a package or research compendium structure — rcompendium-package","title":"Create a package or research compendium structure — rcompendium-package","text":"rcompendium makes easier creation R packages research compendia (.e. predefined files/folders structure) users can focus code/analysis instead wasting time organizing files. full ready--work structure set additional features: version control, remote repository creation, CI/CD configuration (check package integrity several OS, test code 'testthat', build deploy website using 'pkgdown').","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"recommended-workflow","dir":"Reference","previous_headings":"","what":"Recommended workflow","title":"Create a package or research compendium structure — rcompendium-package","text":"Store credentials (given family names, email, ORCID, etc.) set_credentials() (already done); Create new empty RStudio project; Run new_package() create new package structure new_compendium() create new research compendium structure; Edit metadata DESCRIPTION, CITATION, README.Rmd; Start working (add data, write document R functions, etc.); forget commit changes.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"managing-credentials","dir":"Reference","previous_headings":"","what":"Managing credentials","title":"Create a package or research compendium structure — rcompendium-package","text":"can use arguments given, family, email, orcid directly functions new_*() add_*(). create lot projects (packages /compendia) can frustrating long run. alternative way use function set_credentials() permanently store information ~/.Rprofile file. arguments set NULL calling function package, rcompendium search values file. save time (purpose package). Even stored credentials ~/.Rprofile file always able modify --fly (.e. using credentials arguments functions new_*() add_*()) permanently re-running set_credentials().","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"configuring-git","dir":"Reference","previous_headings":"","what":"Configuring git","title":"Create a package or research compendium structure — rcompendium-package","text":"see git correctly configured laptop, run gh::gh_whoami(). see something like:   Otherwise might need run:   See gert::git_config_global_set() information.","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   ... } gert::git_config_global_set(name  = \"user.name\",                              value = \"John Doe\")                              gert::git_config_global_set(name  = \"user.email\",                              value = \"john.doe@domain.com\")                              gert::git_config_global_set(name  = \"github.user\",                              value = \"jdoe\")"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"creating-a-github-repo","dir":"Reference","previous_headings":"","what":"Creating a GitHub repo","title":"Create a package or research compendium structure — rcompendium-package","text":"create GitHub repository directly R, package rcompendium uses function usethis::use_github(), client GitHub REST API. interaction API required authentication method: GITHUB PAT (Personal Access Token). GITHUB PAT locally stored, must: Visit page https://github.com/settings/tokens create new token; Store ~/.Renviron file using usethis::edit_r_environ() adding following line: GITHUB_PAT='ghp_99z9...z9'. Run usethis::gh_token_help() information getting configuring GITHUB PAT. everything well configured, see something like calling gh::gh_whoami():","code":"{   \"name\": \"John Doe\",   \"login\": \"jdoe\",   \"html_url\": \"https://github.com/jdoe\",   \"scopes\": \"repo, workflow\",   \"token\": \"ghp_...z99Z\" }"},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"resources","dir":"Reference","previous_headings":"","what":"Resources","title":"Create a package or research compendium structure — rcompendium-package","text":"Developing R package: https://frbcesab.github.io/rcompendium/articles/developing_a_package.html Working compendium: https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/rcompendium-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create a package or research compendium structure — rcompendium-package","text":"Maintainer: Nicolas Casajus nicolas.casajus@fondationbiodiversite.fr (ORCID) [copyright holder]","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":null,"dir":"Reference","previous_headings":"","what":"Refresh a package/research compendium — refresh","title":"Refresh a package/research compendium — refresh","text":"function removed rcompendium. function refreshes package/research compendium. : Update .Rd files NAMESPACE using devtools::document(); Update external packages (DESCRIPTION file) using add_dependencies(); Update badges README.Rmd (already present); Re-knitr README.Rmd using rmarkdown::render(); Check package integrity using devtools::check(); Run analysis sourcing make.R (compendium).","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Refresh a package/research compendium — refresh","text":"","code":"refresh(compendium = NULL, make = FALSE, check = FALSE, quiet = FALSE)"},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Refresh a package/research compendium — refresh","text":"compendium character length 1. name folder recursively detect dependencies added Imports field DESCRIPTION file. can 'analysis/' (additional folders, .e. data/, outputs/, figures/, etc. created folder), '.' (folders data/, outputs/, figures/, etc. created root project), etc. See new_compendium() information. Default compendium = NULL (.e. additional folder inspected R/, NAMESPACE, vignettes/, tests/ still inspected). make logical value. TRUE Make-like R file make.R sourced. research compendium created new_compendium(). Default FALSE. check logical value. TRUE package integrity checked using devtools::check(). Default FALSE. quiet logical value. TRUE (default) message deleted.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Refresh a package/research compendium — refresh","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/refresh.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Refresh a package/research compendium — refresh","text":"","code":"if (FALSE) { library(rcompendium)  ## Create an R package ---- new_package()  ## Start developing functions ---- ## ...  ## Update package (documentation, dependencies, README) ---- refresh() }"},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":null,"dir":"Reference","previous_headings":"","what":"Store credentials to the .Rprofile — set_credentials","title":"Store credentials to the .Rprofile — set_credentials","text":"function used store user credentials .Rprofile file. Accepted credentials listed . function useful user creates lot packages /research compendiums. .Rprofile file exist function create . Users need paste content clipboard file.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Store credentials to the .Rprofile — set_credentials","text":"","code":"set_credentials(   given = NULL,   family = NULL,   email = NULL,   orcid = NULL,   protocol = NULL )"},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Store credentials to the .Rprofile — set_credentials","text":"given character length 1. given name project maintainer. family character length 1. family name project maintainer. email character length 1. email address project maintainer. orcid character length 1. ORCID project maintainer. protocol character length 1. GIT protocol used communicate GitHub remote. One 'https' 'ssh'. know, keep default value (.e. NULL) protocol 'https'.","code":""},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Store credentials to the .Rprofile — set_credentials","text":"return value.","code":""},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/reference/set_credentials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Store credentials to the .Rprofile — set_credentials","text":"","code":"if (FALSE) { library(rcompendium)   ## Define **ONCE FOR ALL** your credentials ----  set_credentials(\"John\", \"Doe\", \"john.doe@domain.com\",                  orcid = \"9999-9999-9999-9999\", protocol = \"https\") }"},{"path":[]},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-13","dir":"Changelog","previous_headings":"","what":"rcompendium 1.3","title":"rcompendium 1.3","text":"CRAN release: 2023-10-26 Bug fixes get_deps_*() better detects project dependencies delete packages called w/ library(\"pkg\") library('pkg') add_sticker() now copies sticker template compendium Minor changes Provide instructions installing V8 engine Unix systems","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-12","dir":"Changelog","previous_headings":"","what":"rcompendium 1.2","title":"rcompendium 1.2","text":"CRAN release: 2023-10-24 New features get_git_branch_name() detects git branch name add_contributing() adds CONTRIBUTING.md file issue templates add_code_of_conduct() adds CODE_OF_CONDUCT.md file add_github_actions_citation() adds new GitHub action update CITATION.cff file add_github_actions_document() adds new GitHub action update Rd files, NAMESPACE DESCRIPTION files Improvements get_deps_*() better detects project dependencies add_compendium() allows now user choose compendium structure Minor changes Update GitHub Actions templates (yaml files) Update README templates man/ folder NAMESPACE now untracked git (compendium ) Remove dependencies badge README Change default values lifecycle status arguments new_package() Change commit messages new_*() functions (conventional commits) Deprecated refresh() now deprecated deleted new version","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-11","dir":"Changelog","previous_headings":"","what":"rcompendium 1.1","title":"rcompendium 1.1","text":"CRAN release: 2023-04-24 Update GitHub Actions templates (yaml files) Detect current git branch name add_readme_rmd() Ignore renv files (R build GitHub) add_renv()","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-10","dir":"Changelog","previous_headings":"","what":"rcompendium 1.0","title":"rcompendium 1.0","text":"CRAN release: 2022-04-06 New feature: add_dockerfile() creates basic Dockerfile compendium (new argument dokerfile new_compendium()) based rocker/rstudio. New feature: add_renv() initialize renv environment compendium (new argument renv new_compendium()) New feature: add_github_actions_render() automatically render README.md GitHub server push. action triggered README.Rmd modified since last commit. Also add new argument gh_render new_*() functions. New vignette: developing R package New vignette: working compendium Function add_dependencies() allows now missing R/ folder improves detection dependencies vignettes. Function add_lifecycle_badge() copy badge SVG project anymore. image badge now created using https://shields.io/. Update GHA templates. now derived : https://github.com/r-lib/actions/tree/v2-branch/examples Rename default vignette title (title now Get Started) Add cph (copyright holder) tag DESCRIPTION file Change default package hexSticker add R script inst/package-sticker/ easily change hexSticker Rename commits messages (remove emoji) compendium: arguments gh_check website now FALSE default compendium: rename rscripts/ folder analyses/ compendium: delete paper/ folder Review improve documentation Rename templates file names Fix bug: detection nested RStudio projects","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-051","dir":"Changelog","previous_headings":"","what":"rcompendium 0.5.1","title":"rcompendium 0.5.1","text":"CRAN release: 2021-03-24 first submission CRAN: DESCRIPTION file: replace “aim package ‘rcompendium’ make easier…” “Makes easier…” Function set_credentials() write .Rprofile file anymore (allowed CRAN policies). Instead function opens file users need manually paste content clipboard. Replace utils::installed.packages() find.package()","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-05","dir":"Changelog","previous_headings":"","what":"rcompendium 0.5","title":"rcompendium 0.5","text":"Check valid package name Add new features: new_compendium() add_compendium() Allow adding .gitignore .Rbuildignore several names Improve console messages Modify templates","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-041","dir":"Changelog","previous_headings":"","what":"rcompendium 0.4.1","title":"rcompendium 0.4.1","text":"Improve documentation","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-04","dir":"Changelog","previous_headings":"","what":"rcompendium 0.4","title":"rcompendium 0.4","text":"New features: add_testthat(), add_github_actions_codecov(), add_github_actions_codecov_badge(), add_codecov_badge() New arguments new_package(): test codecov Add demo R function pass test show good practices writing functions","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-03","dir":"Changelog","previous_headings":"","what":"rcompendium 0.3","title":"rcompendium 0.3","text":"Improve dependencies detection @examples sections Keep packages versions DESCRIPTION fields Retrieve GitHub pseudo gh::gh_whoami() (github argument)","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-02","dir":"Changelog","previous_headings":"","what":"rcompendium 0.2","title":"rcompendium 0.2","text":"Rename import argument compendium Automatically check dependencies vignettes/ (remove argument suggest) Detect dependencies tests/ Add new internal function path_proj() Use usethis::proj_get() instead ::() Rename add_github_badge() add_github_actions_check_badge() Add new function add_github_actions_pkgdown_badge() Badge functions return now Markdown badges (assigned variable) Badges added end process (adding additional commit) Change default license new_package() Improve inputs checks Change files templates (GH Actions names)","code":""},{"path":"https://frbcesab.github.io/rcompendium/news/index.html","id":"rcompendium-01","dir":"Changelog","previous_headings":"","what":"rcompendium 0.1","title":"rcompendium 0.1","text":"First release package.","code":""}]