Using print(M, tag = 'chart')

The `print(M)` call was missing `print(M, tag = 'chart')`. 

I also made a number of other changes to clean up the document. For example, you were loading a ton of packages that are not used in the index.Rmd. I cleaned this up.

One other suggestion: you probably want to clean up your repo before submitting it. You have a lot of duplicate versions of files and many files could be consolidated into coherent sub-directories. Clear file structure is important for reproducibility as it helps others (and yourself in the future) understand what you did. 

In the future, it would be useful to learn how to use git branching/merging to create alternative versions of files/test changes and, if you like the changes, merge them back into the master branch. This takes a little getting used to at first, but allows you to clearly document the history of a file and avoid all of these Version1, Version2, Version3 . . . files.