Skip to content

Commit

Permalink
Deploying to gh-pages from @ 3ce3e7b 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
@camilavargasp
camilavargasp committed Oct 24, 2024
1 parent 998e69e commit 35d5617
Show file tree
Hide file tree
Showing 84 changed files with 11,315 additions and 11,378 deletions.
Binary file added main/images/lobster_size_lrg_bar_plot.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/images/lobster_size_lrg_dodged_plot.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/images/save-workspace-global-options.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/images/save-workspace.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified main/images/schedule.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
120 changes: 68 additions & 52 deletions main/index.html
View file

Large diffs are not rendered by default.

1,816 changes: 978 additions & 838 deletions main/search.json
View file

Large diffs are not rendered by default.

177 changes: 64 additions & 113 deletions main/session_01.html
View file

Large diffs are not rendered by default.

142 changes: 65 additions & 77 deletions main/session_02.html
View file

Large diffs are not rendered by default.

74 changes: 49 additions & 25 deletions main/session_03.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.53">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>3&nbsp; Git and GitHub Setup – NCEAS coreR for Delta Science Program</title>
<title>3&nbsp; Git and GitHub Setup – NCEAS Learning Hub’s coreR Course</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
Expand Down Expand Up @@ -152,7 +152,7 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
<div class="sidebar-tools-main tools-wide">
<a href="https://www.nceas.ucsb.edu/learning-hub" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-house-door-fill"></i></a>
<a href="https://twitter.com/ucsb_nceas" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
<a href="https://github.com/NCEAS/nceas-training/tree/2024-06-delta" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-github"></i></a>
<a href="https://github.com/NCEAS/nceas-training/tree/2024-10-coreR" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-github"></i></a>
</div>
</div>
</div>
Expand All @@ -166,13 +166,13 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./index.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">About the course</span></a>
<span class="menu-text">Welcome!</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_01.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Welcome: Let’s Talk About Reproducibility</span></span></a>
<span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Course Introduction</span></span></a>
</div>
</li>
<li class="sidebar-item">
Expand All @@ -190,91 +190,115 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_04.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Literate Analysis with Quarto</span></span></a>
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Working in R &amp; RStudio</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_05.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Intro to Git and GitHub</span></span></a>
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Literate Analysis with Quarto</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_06.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Tidy Data</span></span></a>
<span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Reproducibility: a Lego activity</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_07.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Cleaning and Wrangling Data</span></span></a>
<span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Git and GitHub</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_08.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Practice Session I</span></span></a>
<span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Tidy Data</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_09.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Collaborating with Git and GitHub</span></span></a>
<span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Cleaning and Wrangling Data</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_10.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Data Management Essentials</span></span></a>
<span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Practice Session: Joins</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_11.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Publishing your Analysis to the Web</span></span></a>
<span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Collaborating with Git and GitHub</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_12.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Data Visualization</span></span></a>
<span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Publishing to the Web</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_13.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Working with Spatial Data</span></span></a>
<span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Data Visualization</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_14.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Practice Session II</span></span></a>
<span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Practice Session: Collaborative Report</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_15.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Introduction to Shiny</span></span></a>
<span class="menu-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Data Management Essentials</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_16.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Reproducibility and Provenance</span></span></a>
<span class="menu-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Working with Spatial Data</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_17.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Appendix: Install R and Git in your Computer</span></span></a>
<span class="menu-text"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Writing Functions</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_18.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Appendix: Intro to R &amp; RStudio</span></span></a>
<span class="menu-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Practice Session: Functions</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_19.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">19</span>&nbsp; <span class="chapter-title">Office Hour</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_20.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">20</span>&nbsp; <span class="chapter-title">GitHub for Project Management</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_21.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">21</span>&nbsp; <span class="chapter-title">Reproducibility &amp; Provenance</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./session_22.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">22</span>&nbsp; <span class="chapter-title">Installing R and Git in your computer</span></span></a>
</div>
</li>
</ul>
Expand Down Expand Up @@ -426,13 +450,13 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="set-up-global-options-in-
<h4 class="unnumbered anchored" data-anchor-id="set-a-long-timeout-for-the-git-cache">Set a long timeout for the git cache</h4>
<p>Finally, we will run a step that is <strong>only necessary when working on a server</strong>. We need to set our credentials to not time out for a very long time. This is related to how our server operating system handles credentials - not doing this will make your Personal Access Token (PAT, which we will set up in the next section) expire after 15 min on the system, even though it is actually valid for at least a month. <strong>We will do this configuration in the terminal.</strong></p>
<p>You can access the terminal through RStudio by clicking Tools &gt; Terminal &gt; New Terminal.</p>
<div class="callout callout-style-default callout-caution no-icon callout-titled">
<div class="callout callout-style-default callout-caution callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon no-icon"></i>
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
IMPORTANT!!
THIS ONLY NEEDS TO BE RUN ON THE SERVER
</div>
</div>
<div class="callout-body-container callout-body">
Expand Down Expand Up @@ -952,8 +976,8 @@ <h2 data-number="3.3" class="anchored" data-anchor-id="strategy-to-integrate-cha
</a>
</div>
<div class="nav-page nav-page-next">
<a href="./session_04.html" class="pagination-link" aria-label="Literate Analysis with Quarto">
<span class="nav-page-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Literate Analysis with Quarto</span></span> <i class="bi bi-arrow-right-short"></i>
<a href="./session_04.html" class="pagination-link" aria-label="Working in R &amp; RStudio">
<span class="nav-page-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Working in R &amp; RStudio</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
Expand Down
Binary file added main/session_03_files/figure-html/boxplot_ex-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/esc_plot-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/fill_blue-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/fill_blue_geom-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/line_poin_plot-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/theme_bw_plot-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-11-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-12-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-13-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-15-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-19-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-20-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-21-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-22-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-23-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-25-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-26-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-27-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-30-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-32-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added main/session_03_files/figure-html/unnamed-chunk-34-1.png
View file
Binary file added main/session_03_files/figure-html/unnamed-chunk-4-1.png
View file
Binary file added main/session_03_files/figure-html/unnamed-chunk-6-1.png
View file
Binary file modified main/session_03_files/figure-html/unnamed-chunk-7-1.png
View file
Binary file added main/session_03_files/figure-html/unnamed-chunk-8-1.png
View file
Binary file added main/session_03_files/figure-html/unnamed-chunk-9-1.png
View file
Binary file added main/session_03_files/figure-html/violin_plot-1.png
View file
Loading

0 comments on commit 35d5617

Please sign in to comment.