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Now that you have a local version of the repository you can open it back up.
Create a new R markdown script
You will have the default R markdown example
Have a read through this document and then click "Knit HTML" to run it
You have now run an analysis using R markdown
Now since you have created a new file it, your project is now different to what is stored in the remote github repository
Now we need to update the remote repository so others can keep up-to-date
Lets move on to using the github features