Anything labeled LessonX9, where X is a character or a blank space, should be ignored. The final files are of the form Lesson9.
The rmd file might need to be knit several times. It will get about halfway and get stuck on a pruned tree that it says can't be plotted because it is a root. It is not. Knit again. You might have to knit several times. I have knit it up to 15 times in a row to get beyond this stupid error.
And now I can't figure out why the last command to create the random forest from the NHANES diabetes dataset doesn't want to work. Go figure. So I have commented it out.