repo updates pre-submission

[jaytlennon]

@meganllarsen

I'm wondering is we should create a new repo that we use for publication that is more streamlined and matches up with the analyses presented in manuscript.

Some of the analyses and code seem to be missing, or perhaps I wasn't able to find when going through things yesterday.

For example, I don't see bioweb/network related data, code, or output, although I realize this was done in Matlab.

Similarly, we say in the ms that we did cross-correlation in SAS, but I don't see data, code, or output files for that.

[meganllarsen]

@jaytlennon

let's find a time where we can double check all the information between the repo and the ms. two sets of eyes are better than one!