mwpennell / phylopca Goto Github PK

just a reminder:

now that we have a separate suppmat, we should move the supp figures out of the main text and update the refs in the text

nice work everyone. before we submit, we need to do some cleaning of the repo and code as it currently pretty messy.

here is the structure I suggest

doc

• all files to create the ms file

/figs

• figures used in manuscript

analysis

• phylopca.R, phylopca.Rmd, phylopca.md (perhaps set the README file to be equal to the latter). This is the main analyses script which contains all the simulation, data analysis and plotting code

/R

• process-data.R functions for processing empirical data
• analysis-helper.R little functions that are used to help with the analyses

/data

• raw data files for empirical analyses

/output

• results used to generate plots (called by phylopca.R)

I think this would greatly simplify things.

I am still making the sim and results from the mvOU. I will use the rankslope analysis framework to make weakly correlated and highly correlated datasets and still use that same 'shape' of the R matrix. Will not change the alpha matrix, only the R matrix. Will update results shortly. When this analysis is stable, I will merge mvOU sims with the master scritps.