Improving R code useability

[raikens1]

• [ ] set so plots save automatically to separate pdfs when Rmarkdown is knit in workflows_finished
• [x] add code specialized to make each of the figures
• [ ] finish Readme in R code subdirectory
• [ ] purl Rmarkdowns (and test on cluster)
• [x] Add maths explanation to LRT Rmarkdown
• [ ] Sync R code with Markdown methods - some of the R code methods are out of date.
• [x] make R code file for making rate matricies. Right now it's commented out at the bottom of upload_subpops_3mer.R, which is a terrible place.