diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..455da49
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Pat Schloss
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..8b85e91
--- /dev/null
+++ b/README.md
@@ -0,0 +1,3 @@
+# README
+
+This is an RStudio-based version of the materials developed by @frfeng and his [intro-git](https://github.com/frfeng/intro-git) teaching notes
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diff --git a/index.html b/index.html
index 02ea60b..8ec1623 100644
--- a/index.html
+++ b/index.html
@@ -27,21 +27,56 @@
 
 <textarea id="source">
 
-class: center, middle
+## Notes
+* Need to update screenshots with directory structure from the end of bash section see 
 
+.center[![:scale 30%](./images/starting-directory-structure.png)]
 
-# Introduction to 
+* Include .gitignore discussion to show how to hide setup script (did this when teaching on 2023-10-12)
+  * Ignore big data files, PHI, passwords, etc
+  
+* One person had git in a non-standard location that RStudio couldn't find
 
-.center[![:scale 30%](./images/Git-Logo-2Color.png) ]
+---
 
-.center[![:scale 30%](./images/GitHub_Logo.png)]
+## Notes (cont)
+
+* Windows had a pop up window when doing the first git push, had them pick token instead of the other options
+* Windows terminal within RStudio doesn't seem to use bash 
+* When instructor zooms in on RStudio, you lose the labels next to icons (e.g., Commit, Push, Pull)
+* At end, would be good to see how an active research lab uses GitHub to serve up code/data/images for papers
+
+---
+
+## Notes (cont)
+
+* Got through "Modify your R script..." exercise
+  * then talked through why you'd run git from the command line
+  * emphasized that 98% of my git use is covered by RStudio
+  * encouraged to get comfortable using git in RStudio before trying to use git on command line
 
+---
+
+## Notes (cont)
 
+* At the LICENSE part, I showed issue tracker
+* Simulated a conversation with PI
+* Picked the LICENSE
+* Committed changes and closed issue
 
+---
+
+class: center, middle
 
 
+# Introduction to 
+
+.center[![:scale 30%](./images/Git-Logo-2Color.png)]
+
+.center[![:scale 30%](./images/GitHub_Logo.png)]
 
 ---
+
 class: middle, center
 
 ![:scale 56%](./images/phd101212s.gif)
@@ -49,24 +84,42 @@
 
 .tiny[.lightgray[“Piled Higher and Deeper” by Jorge Cham]]
 
-<!-- ---
-# What is Git?
+---
+class: middle, center
 
-.center[![:scale 50%](./images/Git-Logo-2Color.png)]
+.center[![:scale 100%](./images/word-diff.png) ]
 
-<br>
+---
+class: middle, center
 
-Git is a free & open source version control system.
+.center[![:scale 80%](./images/dropbox.png) ]
 
-<br>
+.center[![:scale 80%](./images/google-docs.png)]
 
-.center[[Official website](https://git-scm.com/)] -->
+---
+class: middle, center
+
+.center[![:scale 100%](./images/googlesheets-diff.png) ]
+
+---
+class: middle, center
+
+.center[![:scale 100%](./images/excel-undo.png) ]
 
 ---
 class: middle, center
 
 ![:scale 100%](./images/git-branch.svg)
 
+---
+
+class: middle, center
+
+.center[![:scale 70%](./images/Git-Logo-2Color.png) ]
+
+.center[![:scale 70%](./images/GitHub_Logo.png)]
+
+--
 
 ---
 class: middle, center
@@ -76,12 +129,24 @@
 
 ---
 
+class: middle, center
+
+.center[![:scale 100%](./images/rstudio-new-terminal.png) ]
+
+---
+
+class: middle, center
+
+.center[![:scale 100%](./images/rstudio-terminal.png) ]
+
+---
+
 ### User name
 
 Set a name that is identifiable for credit when review version history.
 
 ```
-$ git config --global user.name "Fred Feng"
+$ git config --global user.name "Pat Schloss"
 ```
 
 --
@@ -91,7 +156,7 @@
 Set an email address that will be associated with each history marker.
 
 ```
-$ git config --global user.email "fredfeng@umich.edu"
+$ git config --global user.email "pdschloss@umich.edu"
 ```
 
 
@@ -109,7 +174,8 @@
 ### On Windows:
 
 ```
-git config --global core.autocrlf true
+
+$ git config --global core.autocrlf true
 ```
 
 
@@ -132,6 +198,13 @@
 
 --
 
+### Credential storage
+
+```
+$ git config --global credential.helper store
+```
+
+---
 
 ### View the configurations
 
@@ -139,314 +212,482 @@
 $ git config --list
 ```
 
+---
+
+## Now to initialize our repository
+
+.center[![:scale 100%](./images/rstudio-git-init-1.png)]
 
 ---
 
-# cd into your .red[un-report] directory
+## Now to initialize our repository
 
+.center[![:scale 75%](./images/rstudio-git-init-2.png)]
 
-To check if you are there, print the working directory
 
-```
-$ pwd
-```
+---
 
-<br>
+## Using git - 98% of what you will do
 
-Or you can list the files in the current directory
+* Get versions of our files into repository
+* Attach a message to our files indicating what happened
 
-```
-$ ls
-```
+.center[![:scale 90%](./images/git-committing.svg)]
 
 ---
-# Show the status of the git repository
 
-```
-$ git status
-```
+## Untracked files
 
-At this point, we will see an error message. 
-This is because the directory is not a git repository yet.
+.center[![:scale 90%](./images/rstudio-git-unstaged.png)]
 
 ---
-# Initialize a new Git repository
 
-```
-$ git init
-```
+## Staging/adding our changes
+
+.center[![:scale 65%](./images/rstudio-git-staged.png)]
 
+Once files checked, click check icon under "Environment" tab name
 
 ---
-# Show the status of the git repository
 
-```
-$ git status
-```
+## Committing our changes
 
-- Show modified files in working directory, staged for your next commit. 
+.center[![:scale 65%](./images/rstudio-git-commit.png)]
 
+Write "Initial commit" in message window
 
 ---
-# Under the hood
 
-Git stores all project info inside a (hidden) .[.git] folder
+## Committing our changes
 
-List all files
+.center[![:scale 65%](./images/rstudio-git-commit-success.png)]
 
-```
-$ ls -a
-```
-
-<br>
+* Click close
+* Notice that the staging window is now empty
 
-List the files inside the .red[.git] folder
+---
 
-```
-$ cd .git
-$ ls
-$ cd ..
-```
+## Create repository in GitHub
 
+- Open the GitHub website and sign in
+- Create a new repository with name .red[un-report]
+  - Do not check the box to add a .red[README] file
+  - Do not select a .red[.gitignore] file 
+  - Do not select a .red[LICENSE] file
+- Click .green[Create repository] button
 
 ---
 
-# Staging area
+## Connecting GitHub to your computer
 
-An intermediate area where a subset of the modified files can be grouped for a commit.
+.center[![:scale 65%](./images/github-push-instructions.png)]
 
-.center[![:scale 90%](./images/git-committing.svg)]
+Make sure that HTTPS is selected and click copy button to the right of the "…or push an existing repository from the command line" section
+
+---
+
+## Connecting GitHub to your computer
 
-It helps to split up unrelated changes in your working directory into multiple, more meaningful commits.
+.center[![:scale 75%](./images/rstudio-git-push-setup.png)]
 
+Enter your GitHub username and wait when asked for your password, we will use a personal access token
 ---
-# Add files to the staging area
 
-```
-$ git add [file_1] [file_2]
-```
+## Create Personal Access Token
 
-Add the files (as they look now) to the staging area for your next commit.
+.center[![:scale 100%](./images/github-dropdown-settings.png) ]
 
-- Each commit should be a logical unit of change.
+---
 
+## Create Personal Access Token
 
+.center[![:scale 100%](./images/github-dropdown-developer-settings.png) ]
 
-<!-- <br>
+---
 
-```
-$ git add .
-```
+## Create Personal Access Token
+
+.center[![:scale 100%](./images/github-dropdown-pat-settings.png) ]
+
+---
 
-Add all files in working directory to the staging area. -->
+## Create Personal Access Token
 
+.center[![:scale 100%](./images/github-generate-pat.png) ]
 
 ---
-# Commit (i.g., taking a snapshot of) the changes from the staged files
 
+## Create Personal Access Token
 
+.center[![:scale 100%](./images/github-new-access-token-1.png) ]
 
-```
-$ git commit -m "Initial commit"
-```
+---
+
+## Create Personal Access Token
+
+.center[![:scale 100%](./images/github-new-access-token-2.png) ]
 
 ---
-class: middle, center 
 
-# Tracking changes
+## Connecting GitHub to your computer
+
+.center[![:scale 55%](./images/rstudio-git-push-setup-w-pat.png)]
+
+* Where asked for your password paste the personal access token
+* We shouldn't be asked for password again for 90 (or whatever) days
 
 
 ---
-Let's create a file called .blue[notes.txt].
 
+## New file
+
+GitHub suggests adding a README file, let's do it from within RStudio
+
+.center[![:scale 55%](./images/rstudio-new-markdown.png) ]
+
+
+Save the file as .blue[README.md]
+
+---
+## Let's type some text into the .blue[README.md] file
 
 ```
-$ nano notes.txt
+## Notes for UN Report 
+
+We plotted life expectancy over time.
 ```
+  
+--
 
-Let's type some text into the .blue[notes.txt] file
+Check out the change in the git staging window
 
+.center[![:scale 50%](./images/rstudio-readme-unstaged.png) ]
 
->> .green[*We plotted life expectancy over time.*]
+---
 
+## Stage, add and commit the change
 
-We can verify the file was created by running
+.center[![:scale 100%](./images/rstudio-readme-commit-1.png) ]
+
+---
+## Let's add a line to README.md
 
 ```
-$ ls
+We plotted life expectancy over time.
+Each point represents a country
 ```
 
-We can also view the content of the file in the command line window by running
+--
+Notice the change in the git staging window
 
-```
-$ cat notes.txt
-```
+.center[![:scale 100%](./images/rstudio-readme-stage-modify.png) ]
 
 ---
-# Commit the changes
 
-```
-$ git status
-```
+## Commit the new changes
 
-```
-$ git add notes.txt
-```
+.center[![:scale 60%](./images/rstudio-readme-commit-2.png) ]
 
-```
-$ git status
-```
+Notice the "diff" at the bottom of the window indicating what has changed
 
-```
-$ git commit -m "Start notes on analysis"
-```
+---
+
+## Exercise
+
+Follow the previous examples to...
+
+- Add a third line to the README.md
 
 ```
-git status
+We plotted life expectancy over time.
+Each point represents a country.
+Continents are grouped by color.
 ```
 
+- Stage and commit the above change
+
+- What happens if you click "View file @ XYZ1234" in the "Changes" view of an
+earlier commit? When would you want to use this?
+
 ---
-# Make some more changes
 
-```
-$ nano notes.txt
-```
+## Exercise
+
+Which of the following commit messages would be most appropriate for the last commit?
+
+1. “Changes”
+1. “Added line ‘Continents are grouped by color.’ to notes.txt”
+1. “Describe grouping”
+
+---
+class: middle, center
+
+
+.center[![:scale 100%](./images/git_commit_2x.png)]
 
 <br>
 
-Let's add a second line into the .blue[notes.txt] file
+.lightgray[Source: https://xkcd.com/1296/]
+
 
+---
 
->> .gray[*We plotted life expectancy over time.*]
+## Show the commit logs
 
->> .green[*Each point represents a country.*]
+.center[![:scale 75%](./images/rstudio-git-history.png)]
 
+---
 
-<br>
+## Let's edit our README.md file further
 
-```
-$ cat notes.txt
-```
+.center[![:scale 80%](./images/rstudio-readme-edit.png)]
 
 ---
-# Commit the new changes
 
-```
-$ git status
-```
+## Let's check out the diff before committing
 
-```
-$ git diff
-```
+.center[![:scale 80%](./images/rstudio-readme-diff.png)]
 
-```
-$ git add notes.txt
-```
+---
 
-```
-$ git commit -m "Add information on points"
-```
+## Let's stage and commit from the diff window
 
-```
-$ git status
-```
+.center[![:scale 80%](./images/rstudio-readme-paragraph-commit.png)]
 
 ---
-# Exercise
 
-Follow the previous examples to 
+## How to get this up to GitHub?
 
-- Add a third line to the .blue[notes.txt] file
+.green[Push]. Click the upward pointing arrow.
 
->> .gray[*We plotted life expectancy over time.*]
+.center[![:scale 80%](./images/rstudio-readme-push.png)]
+
+---
 
->> .gray[*Each point represents a country.*]
+## GitHub changes
 
->> .green[*Continents are grouped by color..*]
+.center[![:scale 100%](./images/github-readme-push.png)]
 
+---
 
+## GitHub commit history
 
-- Commit the above change. 
+.center[![:scale 100%](./images/github-commit-history.png)]
 
 
 ---
 
-# Question
+## GitHub diffs
 
-Which of the following commit messages would be most appropriate for the last commit?
+.center[![:scale 100%](./images/github-commit-diff.png)]
 
-1. “Changes”
-1. “Added line ‘Continents are grouped by color.’ to notes.txt”
-1. “Describe grouping”
+---
+
+## Let's create a file on GitHub
 
+.center[![:scale 100%](./images/github-create-new-file.png)]
 
 ---
-class: middle, center
 
+## Let's create a file on GitHub
 
-![:scale 100%](./images/git_commit_2x.png)
+.center[![:scale 100%](./images/github-name-file-license.png)]
 
-<br>
 
-.lightgray[Source: https://xkcd.com/1296/]
+---
+
+## Let's create a file on GitHub
+
+.center[![:scale 100%](./images/github-ignore-warning.png)]
 
 
 ---
 
-# Show the commit logs
+## Let's create a file on GitHub
 
-```
-$ git log
-```
+.center[![:scale 100%](./images/github-select-license.png)]
+
+---
+
+## Let's create a file on GitHub
+
+.center[![:scale 100%](./images/github-license-text.png)]
+
+---
+
+## Let's commit changes on GitHub
+
+.center[![:scale 100%](./images/github-license-commit.png)]
+
+---
+
+## New file already on GitHub
+
+.center[![:scale 100%](./images/github-repo-update.png)]
+
+---
+
+## How do we get our file back to our local computer?
+
+.center[![:scale 100%](./images/rstudio-pre-pull.png)]
+
+
+---
+
+## How do we get our file back to our local computer? .red[Pull]
+
+.center[![:scale 100%](./images/rstudio-post-pull.png)]
 
-```
-$ git log -5
-```
+
+---
+
+## Exercise
+
+* Modify your R script to include the following after the ggplot code chunk:
 
 ```
-$ git log --oneline
+ggsave("figures/gdpPercap_lifeExp.png")
 ```
 
+* Rerun the ggplot code chunk along with the following ggsave line
+* Update your REAMDE.md file
+* Stage the changes and new file, commit those changes, and push to GitHub
 
+---
+
+## Exercise
+
+* Create a new Git repository on your computer called workshop
+* Write three lines about what you have learned about R and bash a file called README.md, commit your changes
+* Modify one line, add a fourth line
+* Display the differences between its updated state and its original state
+* Push it to GitHub
 
 ---
-class: middle, center
 
-# Intro to GitHub
+## Why run git from the terminal?
+
+* RStudio and other git-based tools with a graphical user interface (GUI) have
+gotten really good over the past few years, especially for most of our needs
+
+--
+
+* But they aren't as powerful as running the commands from the command line
+--
+
+* Believe it or not, typing can be a lot faster than pointing and clicking!
+
+--
+
+* If you need help doing something, Google likely point you to 
+solutions using the command line
+--
+
+* You don't always have access to a GUI (e.g., HPC)
 
 ---
 
-- Open the GitHub website and sign in
-- Create a new repository with name .red[un-report]
-  - Do not check the box to add a README file
-- Copy the URL that ends with .red[un-report.git]
-- Add this GitHub repo we just created as a "remote" for our local git repo.
+## git from the terminal
+
+How do we look at the staging area?
 
 ```
-$ git remote add [alias] [url]
+$ git status
 ```
 
-By convention the GitHub repo is often named .red[origin].
+--
+
+Modify README.md to include your name and the date
 
 ```
-$ git remote add origin https://github.com/x/abc.git
+$ git status
 ```
 
+--
+
+See the change as git sees it
+
+```
+$ git diff
+```
 
 ---
 
+## git from the terminal
+
+To stage the change (can add more than one file)
+
 ```
-$ git clone [url]
+$ git add README.md 
+$ git status
 ```
 
+--
+
+To commit the change
+
 ```
-$ git push origin main
+$ git commit -m "Added my name and date"
+$ git status
 ```
 
+---
+
+## git from the terminal
+
+To push the changes
+
 ```
-$ git pull origin main
+$ git push
+$ git status
 ```
 
+--
+To pull any changes (there aren't any)
+```
+$ git pull
+```
+
+Why might you want to pull from GitHub before committing any changes on your
+local computer?
+
+---
+
+## Exercise
+
+* Change the ColorBrewer palette to `Dark2`
+* Rerun the code and be sure to save the output with `ggsave`
+* Use `git status` to look at the staging area
+* Use `git diff` to look at what has changed
+* Stage, commit, and push your changes
+
+---
+
+## Collaboration
+
+.center[![:scale 100%](./images/github-collaborators.png)]
+
+---
+
+## Collaboration
+
+.center[![:scale 100%](./images/github-collaborators-add.png)]
+
+---
+
+## Collaboration
+
+.center[![:scale 100%](./images/github-collaborators-waiting.png)]
+
+---
+
+## From here...
+
+* Option 1: Fork repository / Create project from repository / Push / File pull request
+* Option 2: Clone repository to new project / Push to main user's repository
+* Option 3: Create feature branch / Clone repository to new project / Work on new feature branch / Push to main user's repository / Merge branches
+
+Cover how to handle merge conflicts?
 
 <!-- ------------------------------------------ -->
 
@@ -487,4 +728,4 @@
 <script>mermaid.initialize({startOnLoad:true});</script>
 
 </body>
-</html>
\ No newline at end of file
+</html>