logo

Author: libjohn

_site.yml

@@ -5,22 +5,29 @@ description: |
 # exclude:
 #   - README.md
 #   - license.md
+# favicon: logo.png
 navbar:
 #  title: "RStudio & Version Control"
+  logo:
+    image: libs-local/rfun_logo.png
+    href: https://rfun.library.duke.edu
   left:
     - text: "Resources"
       href: "resources.html"
+  # logo:
+  #   image: libs-local/rfun_logo.png
+  #   href: https://rfun.library.duke.edu    
   right:
     - icon: fa-github
 #    - text: "GitHub"
       href: https://github.com/data-and-visualization/git-tutorial/         
 #     - icon: fa-home
-    - text: "Home"
-      menu:
-        - text: "Rfun Home"
-          href: "https://rfun.library.duke.edu/"
-        - text: "CDVS Home"
-          href: https://library.duke.edu/data/     
+# #    - text: "Home"
+#       menu:
+#         - text: "Rfun Home"
+#           href: "https://rfun.library.duke.edu/"
+#         - text: "CDVS Home"
+#           href: https://library.duke.edu/data/   
 output_dir: docs
 output:
   distill::distill_article:

docs/index.html

@@ -2047,24 +2047,16 @@ <h3>${suggestion.title}</h3>
 <header class="header header--fixed" role="banner">
 <nav class="distill-site-nav distill-site-header">
 <div class="nav-left">
+<a class="logo" href="https://rfun.library.duke.edu">
+<img src="libs-local/rfun_logo.png" alt="Logo"/>
+</a>
 <a href="index.html" class="title">RStudio &amp; Version Control</a>
 <a href="resources.html">Resources</a>
 </div>
 <div class="nav-right">
 <a href="https://github.com/data-and-visualization/git-tutorial/">
 <i class="fa fa-github" aria-hidden="true"></i>
 </a>
-<div class="nav-dropdown">
-<button class="nav-dropbtn">
-Home
- 
-<span class="down-arrow">&#x25BE;</span>
-</button>
-<div class="nav-dropdown-content">
-<a href="https://rfun.library.duke.edu/">Rfun Home</a>
-<a href="https://library.duke.edu/data/">CDVS Home</a>
-</div>
-</div>
 <a href="javascript:void(0);" class="nav-toggle">&#9776;</a>
 </div>
 </nav>
@@ -2083,7 +2075,7 @@ <h1>Git, GitHub &amp; RStudio</h1>
 
 <div class="d-article">
 <p>Using RStudio to manage version control got a lot easier with the version 2.x release of the <a href="https://usethis.r-lib.org/"><code>usethis</code></a> package. Therefore, this site now consists of links and tips.</p>
-<p>After <code>usethis</code> setup, take your reproducibility to the next level. <a href="https://guides.github.com/activities/citable-code/">Make your code citable</a> by connecting your GitHub repo and your <a href="https://orcid.org/register">ORCHID</a> (unique author ID) to the <a href="https://zenodo.org/">Zenodo</a> archival repository. This way, every time you commit a milestone release, you can mint a new DOI. Then, put your repository into a binder.org container with the <code>holepunch</code> package.</p>
+<p>After <code>usethis</code> setup, take your reproducibility to the next level. <a href="https://guides.github.com/activities/citable-code/">Make your code citable</a> by connecting your GitHub repo and your <a href="https://orcid.org/register">ORCID</a> (unique author ID) to the <a href="https://zenodo.org/">Zenodo</a> archival repository. This way, every time you commit a milestone release, you can mint a new DOI. Then, put your repository into a binder.org container with the <code>holepunch</code> package.</p>
 <h3 id="setup">Setup</h3>
 <p>To get started, get a free GitHub.com account. Make sure you have the latest versions of R, RStudio, (Rtools if you’re Windows), and usethis. Then, you need to setup your RStudio configuration. Two key documents will help: <a href="https://usethis.r-lib.org/articles/articles/usethis-setup.html">Setup</a>, and <a href="https://usethis.r-lib.org/articles/articles/git-credentials.html">Managing Git(Hub) Credentials</a></p>
 <h3 id="tips">Tips</h3>

docs/libs-local/rfun_logo.png

@@ -2044,24 +2044,16 @@ <h3>${suggestion.title}</h3>
 <header class="header header--fixed" role="banner">
 <nav class="distill-site-nav distill-site-header">
 <div class="nav-left">
+<a class="logo" href="https://rfun.library.duke.edu">
+<img src="libs-local/rfun_logo.png" alt="Logo"/>
+</a>
 <a href="index.html" class="title">RStudio &amp; Version Control</a>
 <a href="resources.html">Resources</a>
 </div>
 <div class="nav-right">
 <a href="https://github.com/data-and-visualization/git-tutorial/">
 <i class="fa fa-github" aria-hidden="true"></i>
 </a>
-<div class="nav-dropdown">
-<button class="nav-dropbtn">
-Home
- 
-<span class="down-arrow">&#x25BE;</span>
-</button>
-<div class="nav-dropdown-content">
-<a href="https://rfun.library.duke.edu/">Rfun Home</a>
-<a href="https://library.duke.edu/data/">CDVS Home</a>
-</div>
-</div>
 <a href="javascript:void(0);" class="nav-toggle">&#9776;</a>
 </div>
 </nav>

docs/resources.html

@@ -5,15 +5,15 @@
       "title": "Git, GitHub & RStudio",
       "description": "Makin' it work!!",
       "author": [],
-      "contents": "\r\nUsing RStudio to manage version control got a lot easier with the version 2.x release of the usethis package. Therefore, this site now consists of links and tips.\r\nAfter usethis setup, take your reproducibility to the next level. Make your code citable by connecting your GitHub repo and your ORCHID (unique author ID) to the Zenodo archival repository. This way, every time you commit a milestone release, you can mint a new DOI. Then, put your repository into a binder.org container with the holepunch package.\r\nSetup\r\nTo get started, get a free GitHub.com account. Make sure you have the latest versions of R, RStudio, (Rtools if you’re Windows), and usethis. Then, you need to setup your RStudio configuration. Two key documents will help: Setup, and Managing Git(Hub) Credentials\r\nTips\r\nClone or fork from GitHub\r\nusethis::create_from_github(\"https://github.com/data-and-visualization/git-tutorial\")\r\nCreate the GitHub repo from local\r\nlibrary(usethis)\r\nuse_git()          # initialize a git repo\r\nuse_git_ignore()\r\nuse_readme.Rmd()\r\nuse_ccby_license()\r\nuse_github()       # Connect local repo to GitHub\r\nset-up git and manage GitHub credentials\r\n# Sign-in to your GitHub account\r\n# Read: https://usethis.r-lib.org/articles/articles/git-credentials.html\r\n# Read: https://usethis.r-lib.org/articles/articles/usethis-setup.html\r\nusethis::create_github_token()\r\ngitcreds::gitcreds_set()\r\ngh::gh_whoami()\r\nusethis::git_sitrep()\r\nusethis::use_git_config(user.name = \"Jane Doe\", user.email = \"[email protected]\")\r\ngh::git_sitrep()\r\nPublish your code in a binder.org container\r\nUse the holepunch package\r\nlibrary(holepunch)\r\n\r\nwrite_compendium_description()\r\nwrite_dockerfile()\r\ngenerate_badge()\r\nbuild_binder()\r\n\r\nThe old documentation from this site can be found in the v.0.2019 release on GitHub.\r\n\r\n\r\n\r\n",
-      "last_modified": "2020-12-17T17:01:43-05:00"
+      "contents": "\r\nUsing RStudio to manage version control got a lot easier with the version 2.x release of the usethis package. Therefore, this site now consists of links and tips.\r\nAfter usethis setup, take your reproducibility to the next level. Make your code citable by connecting your GitHub repo and your ORCID (unique author ID) to the Zenodo archival repository. This way, every time you commit a milestone release, you can mint a new DOI. Then, put your repository into a binder.org container with the holepunch package.\r\nSetup\r\nTo get started, get a free GitHub.com account. Make sure you have the latest versions of R, RStudio, (Rtools if you’re Windows), and usethis. Then, you need to setup your RStudio configuration. Two key documents will help: Setup, and Managing Git(Hub) Credentials\r\nTips\r\nClone or fork from GitHub\r\nusethis::create_from_github(\"https://github.com/data-and-visualization/git-tutorial\")\r\nCreate the GitHub repo from local\r\nlibrary(usethis)\r\nuse_git()          # initialize a git repo\r\nuse_git_ignore()\r\nuse_readme.Rmd()\r\nuse_ccby_license()\r\nuse_github()       # Connect local repo to GitHub\r\nset-up git and manage GitHub credentials\r\n# Sign-in to your GitHub account\r\n# Read: https://usethis.r-lib.org/articles/articles/git-credentials.html\r\n# Read: https://usethis.r-lib.org/articles/articles/usethis-setup.html\r\nusethis::create_github_token()\r\ngitcreds::gitcreds_set()\r\ngh::gh_whoami()\r\nusethis::git_sitrep()\r\nusethis::use_git_config(user.name = \"Jane Doe\", user.email = \"[email protected]\")\r\ngh::git_sitrep()\r\nPublish your code in a binder.org container\r\nUse the holepunch package\r\nlibrary(holepunch)\r\n\r\nwrite_compendium_description()\r\nwrite_dockerfile()\r\ngenerate_badge()\r\nbuild_binder()\r\n\r\nThe old documentation from this site can be found in the v.0.2019 release on GitHub.\r\n\r\n\r\n\r\n",
+      "last_modified": "2020-12-17T18:10:27-05:00"
     },
     {
       "path": "resources.html",
       "title": "Resources",
       "author": [],
       "contents": "\r\nSocial Coding Sites\r\nhttps://github.com\r\nhttps://gitlab.com\r\nhttps://bitbucket.org\r\nDuke’s GitLab Instance\r\nManaging SSH keys\r\n\r\nGUI Git Clients\r\nRStudio – Free. Great for useRs\r\nSublime’s Merge – Downloaded and evaluated for free. $100 / 3-years of upgrades.\r\nGitKracken – Free if you have the GitHub Student Pack or the GitHub Teacher toolbox\r\nSourceTree – Free. (defaults to use with BitBucket)\r\nUsethis Package\r\nhttps://usethis.r-lib.org/\r\nFree Book\r\nHappy Git and GitHub for the useR\r\nHandy Article\r\n10 Common Problems / Solutions\r\nReproducibility\r\nWriting clear code: Tools for Reproducible Research\r\nInitial Steps Toward Reproducible Research\r\nMaking your research reproducible with TIER + R + GitHub [Slides]. Cetinkaya-Rundel, M. (2016). Open Science Framework. Retrieved from https://osf.io/phyau\r\n\r\n\r\n\r\n",
-      "last_modified": "2020-12-17T17:01:44-05:00"
+      "last_modified": "2020-12-17T18:10:27-05:00"
     }
   ],
   "collections": []

docs/search.json

@@ -14,7 +14,7 @@ knitr::opts_chunk$set(echo = FALSE)
 
 Using RStudio to manage version control got a lot easier with the version 2.x release of the [`usethis`](https://usethis.r-lib.org/) package.  Therefore, this site now consists of links and tips.
 
-After `usethis` setup, take your reproducibility to the next level.  [Make your code citable](https://guides.github.com/activities/citable-code/) by connecting your GitHub repo and your [ORCHID](https://orcid.org/register) (unique author ID) to the [Zenodo](https://zenodo.org/) archival repository.  This way, every time you commit a milestone release, you can mint a new DOI.  Then, put your repository into a binder.org container with the `holepunch` package.
+After `usethis` setup, take your reproducibility to the next level.  [Make your code citable](https://guides.github.com/activities/citable-code/) by connecting your GitHub repo and your [ORCID](https://orcid.org/register) (unique author ID) to the [Zenodo](https://zenodo.org/) archival repository.  This way, every time you commit a milestone release, you can mint a new DOI.  Then, put your repository into a binder.org container with the `holepunch` package.
 
 ### Setup