Code to model phylogenetic rate and allelic stationary distribution parameters as function of genomic covariates. Alleles are represented as condtional probabilities, P(data|allelic state). Allele with only a single value (such as DNA) can be represented by a one-hot encoded vector per-site per-species (e.g. A=[1 0 0 0]).
Package can be installed with the following line of code:
devtools::install_github("ndukler/phyloGLM")
NOTE: Please pull changes/re-install regularly, this package is still relatively new and as such, bugfixes and features are being added regularly.
A prebuilt version of the vignette is published here (http://rpubs.com/ndukler/phyloGLMIntro) but if you want to rebuild the included vignette to ensure that it is up to date, use:
devtools::install_github("ndukler/phyloGLM", build_vignettes = TRUE)
WARNING: This will take a few minutes.
Acknowledgements: I would like to thank Nicholas Matzke for useful discussions (https://github.com/nmatzke) and Meabh McCurdy (https://github.com/MeabhMcCurdy) from whom I borrowed and modified code to use expokit routines in c++.