mwpennell / phylopca Goto Github PK
View Code? Open in Web Editor NEWcode and manuscript for phylo pca paper
License: GNU General Public License v2.0
code and manuscript for phylo pca paper
License: GNU General Public License v2.0
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.
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
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 codeprocess-data.R
functions for processing empirical dataanalysis-helper.R
little functions that are used to help with the analysesphylopca.R
)I think this would greatly simplify things.
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