Add Show notes and cleanup structure

Notes.Rmd

@@ -0,0 +1,29 @@
+---
+title: "Show Notes"
+output: html_document
+editor_options:
+  chunk_output_type: console
+---
+
+# Navigate R Studio and Setup Project
+
+  * Open RStudio
+  * Create a new "New Project" in `~/work`
+    * If you use Git (you should) use "New Project" -> "Version Control" -> "Git".
+    * "File" -> "New Project" -> "New Directory" -> "New Project" -> "work/skc-workshop". Projects and data must be saved in `~/work` otherwise they will be lost.  Use a good name such as "skc-workshop"
+  * Turn off saving `.RData` in workspace
+    * "Tools" -> "Global Options" -> "General" (already selected) -> "Basic" (already selected) -> Under "Workspace" turn off "Restore `.RData` …" and set "Save workspace to `.RData` …" to "Never"
+  * Create a new "R Markdown" File
+    * "File" -> "New File" -> "R Markdown" -> "Create Empty Document" (bottom left button).
+    * Save file (cmd-s for Mac, ctrl-s for Windows/Linux) and use a good name such as "R-Ecology-Workshop" (it will add the `.Rmd` extension)
+  * Write, Setup, and View RMarkdown
+    * Write title `# RStudio` 
+    * "Settings (gear)" -> "Preview in Viewer Pane"
+    * "Settings (gear)" -> "Chunk Output in Console"
+    * Save file
+    * Knit (Knit to HTML)
+    * Optionally set "Knit on Save" - (runs entire notebook)
+
+Resources:
+
+  * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html

prep/Setup.html → Notes.html

@@ -11,7 +11,7 @@
 
 
 
-<title>Setup</title>
+<title>Show Notes</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -348,58 +348,53 @@
 
 
 
-<h1 class="title toc-ignore">Setup</h1>
+<h1 class="title toc-ignore">Show Notes</h1>
 
 </div>
 
 
-<div id="setup" class="section level1">
-<h1>Setup</h1>
-<p>Update Tools with “Tools -&gt; Update” (do not pin) - takes a long
-time - don’t do in class.</p>
-<p>Use a “R Markdown” document (<code>output: html_document</code> in
-prolog).</p>
-<p>To have the output display in the console (not inline) set in the
-config for the Rmd file set “chunk output in console”.</p>
-<p>To view Rmd rendered (click Knit to html) in separate windows select
-settings for the Rmd file (wheel) and select “Preview in Window”</p>
-<p>Prolog should look like this:</p>
-<pre><code>---
-title: &quot;Setup&quot;
-output: html_document
-editor_options:
-  chunk_output_type: console
----</code></pre>
-<div id="git" class="section level2">
-<h2>Git</h2>
-<p>Setup Git</p>
-<pre class="bash"><code>git config color.ui auto
-git config pull.ff only
-git config push.default simple
-
-#git config user.name &quot;First Last&quot;
-#git config user.email &quot;first_last@example.edu&quot;</code></pre>
-<p>Notes:</p>
+<div id="navigate-r-studio-and-setup-project" class="section level1">
+<h1>Navigate R Studio and Setup Project</h1>
 <ul>
-<li>R Notebooks seem fragile and Caching output seems dangerous. Use
-“Chunk Output Inline” for a more Notebook experence or use Juypter!</li>
-<li>R Markdown is a bit different (lists for example) than other
-markdown.</li>
-<li>With Rmd files I am a fan of using the console (chunk output in
-console) and use cmd-enter to run each line (opt-enter for not advancing
-cursor) for development.</li>
+<li>Open RStudio</li>
+<li>Create a new “New Project” in <code>~/work</code>
+<ul>
+<li>If you use Git (you should) use “New Project” -&gt; “Version
+Control” -&gt; “Git”.</li>
+<li>“File” -&gt; “New Project” -&gt; “New Directory” -&gt; “New Project”
+-&gt; “work/skc-workshop”. Projects and data must be saved in
+<code>~/work</code> otherwise they will be lost. Use a good name such as
+“skc-workshop”</li>
+</ul></li>
+<li>Turn off saving <code>.RData</code> in workspace
+<ul>
+<li>“Tools” -&gt; “Global Options” -&gt; “General” (already selected)
+-&gt; “Basic” (already selected) -&gt; Under “Workspace” turn off
+“Restore <code>.RData</code> …” and set “Save workspace to
+<code>.RData</code> …” to “Never”</li>
+</ul></li>
+<li>Create a new “R Markdown” File
+<ul>
+<li>“File” -&gt; “New File” -&gt; “R Markdown” -&gt; “Create Empty
+Document” (bottom left button).</li>
+<li>Save file (cmd-s for Mac, ctrl-s for Windows/Linux) and use a good
+name such as “R-Ecology-Workshop” (it will add the <code>.Rmd</code>
+extension)</li>
+</ul></li>
+<li>Write, Setup, and View RMarkdown
+<ul>
+<li>Write title <code># RStudio</code></li>
+<li>“Settings (gear)” -&gt; “Preview in Viewer Pane”</li>
+<li>“Settings (gear)” -&gt; “Chunk Output in Console”</li>
+<li>Save file</li>
+<li>Knit (Knit to HTML)</li>
+<li>Optionally set “Knit on Save” - (runs entire notebook)</li>
+</ul></li>
+</ul>
+<p>Resources:</p>
+<ul>
+<li><a href="https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html" class="uri">https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html</a></li>
 </ul>
-</div>
-</div>
-<div id="test" class="section level1">
-<h1>Test</h1>
-<p>Top/bottom</p>
-<pre class="r"><code>1+2</code></pre>
-<pre><code>## [1] 3</code></pre>
-<pre class="r"><code>3+4</code></pre>
-<pre><code>## [1] 7</code></pre>
-<pre class="r"><code>print(&#39;Hello World&#39;)</code></pre>
-<pre><code>## [1] &quot;Hello World&quot;</code></pre>
 </div>
 
 

ReadMe.md

@@ -1 +1,14 @@
 # SKC Carpentries Workshop June 2024
+
+## Lessons
+
+Lessons (Day 1):
+  * https://datacarpentry.org/R-ecology-lesson-alternative/index.html
+  * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html
+  * https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html
+  * https://datacarpentry.org/R-ecology-lesson-alternative/how-r-thinks-about-data.html
+
+Lessons (Day 2):
+  * https://datacarpentry.org/R-ecology-lesson-alternative/working-with-data.html
+  * https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html
+

env.sh

@@ -2,6 +2,10 @@
 # Setup shell with:
 # . ./env.sh
 
+if [ -z "$USER" ] ; then
+    export USER=$NB_USER
+fi
+
 export SSH_AUTH_SOCK=/run/lock/agent.$USER
 if [ ! -S $SSH_AUTH_SOCK ] ; then
     eval `ssh-agent -a $SSH_AUTH_SOCK` | grep -v "^Agent pid"

prep/Setup.Rmd → prep/Instructor_Notes.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Setup"
+title: "Instructor Notes"
 output: html_document
 editor_options:
   chunk_output_type: console
@@ -25,6 +25,9 @@ editor_options:
 ---
 ```
 
+Project should use a "R Project". Load by clicking on the `.RProj` file.
+
+
 ## Git
 
 Setup Git
@@ -38,7 +41,7 @@ git config push.default simple
 #git config user.email "first_last@example.edu"
 ```
 
-Notes:
+## Notes
 
   * R Notebooks seem fragile and Caching output seems dangerous.  Use "Chunk Output Inline" for a more Notebook experence or use Juypter!
   * R Markdown is a bit different (lists for example) than other markdown.

Overview.ipynb → prep/Notebook.ipynb

@@ -2,16 +2,24 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "898b87d6-96c4-4c9b-9713-fde12d72c176",
+   "id": "bad274ce-122f-4a4f-85e4-d5716a15e557",
    "metadata": {},
    "source": [
-    "# SKC JupyterLab"
+    "# Setup Notebook"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "71db22fe-b816-43c2-aab9-4b36ee2d6f10",
+   "metadata": {},
+   "source": [
+    "## Test"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "bff3dc73-02d1-49de-a397-eb086ac17c33",
+   "id": "1ea83d46-645e-4dd5-a6c2-dc74967037b9",
    "metadata": {},
    "outputs": [
     {
@@ -27,26 +35,10 @@
     "print(sys.version)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "96eedf95-e36d-45af-84a3-ef53016628f9",
-   "metadata": {},
-   "source": [
-    "Lessons (Day 1):\n",
-    "* https://datacarpentry.org/R-ecology-lesson-alternative/index.html\n",
-    "* https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html\n",
-    "* https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html\n",
-    "* https://datacarpentry.org/R-ecology-lesson-alternative/how-r-thinks-about-data.html\n",
-    "\n",
-    "Lessons (Day 2):\n",
-    "* https://datacarpentry.org/R-ecology-lesson-alternative/working-with-data.html\n",
-    "* https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8d33cae3-32d9-431a-b806-0556792fb840",
+   "id": "b6ec5b43-6626-4d3b-b5a6-25c74a81b19b",
    "metadata": {},
    "outputs": [],
    "source": []

prep/Preparation.Rmd → prep/RStudio.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Preparation"
+title: "Lesson Preparation"
 output: html_document
 editor_options: 
   chunk_output_type: console