From ba8df4c269d78fa261433e5b054999f78baa7909 Mon Sep 17 00:00:00 2001
From: Timothy Middelkoop <tmiddelkoop@internet2.edu>
Date: Tue, 4 Jun 2024 09:36:02 -0500
Subject: [PATCH] Refine project setup

---
 Notes.md | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/Notes.md b/Notes.md
index 7c3f2d8..b728aed 100644
--- a/Notes.md
+++ b/Notes.md
@@ -48,6 +48,17 @@
 ## Navigate R Studio and Setup Project
 
   * Open RStudio
+  * Setup Git
+    * This needs to be done only once when you first use the environment.
+    * Click on the "Terminal"
+      * Run (note the quotes and replace with your information) the following in the terminal:
+```bash
+git config --global user.name "First Last"
+git config --global user.email "first_last@skc.edu"
+git config --global credential.helper store
+git config --global core.editor nano
+git config --global --list
+```
   * Create a new "New Project" in `~/work` with "Git"
     * Note: Projects and data must be saved in `~/work` otherwise they will be lost.  
     * Select "Version Control" -> "Git"
@@ -55,6 +66,7 @@
       * Project directory name: leave blank
       * Create project as a subdirectory of: ~/work (click "Browse" to change)
       * Click "Create Project"
+      * When prompted enter your user_name and use the newly created "personal access token" as the password.
   * Turn off saving `.RData` in project (not workspace)
     * It is not good to save data, especially in git.
     * "Tools" -> "Project Options" 
@@ -63,17 +75,6 @@
       * Set "Save workspace to .RData on exit" to "No"
       * Set "Always save history" to "No"
       * Click "Ok"
-  * Setup Git
-    * This needs to be done only once when you first use the environment.
-    * Click on the "Terminal"
-      * Run (note the quotes and replace with your information) the following in the terminal:
-```bash
-git config --global user.name "First Last"
-git config --global user.email "first_last@skc.edu"
-git config --global credential.helper store
-git config --global core.editor nano
-git config --global --list
-```
   * Create a new "R Markdown" file
     * "File" -> "New File" -> "R Markdown" -> Click "Create Empty Document" (bottom left button).
     * Save file ("R-Ecology"):