Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data is available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data.
In this package we have implemented a simple solution to increase the overlap while avoiding potential the biases introduced by imputing data. If some external topological or taxonomic information is available, this can be used to maximize the overlap between the data and the phylogeny. The algorithms in phyndr replace a species lacking data with a species that has data. This swap can be made because for those two species, all phylogenetic relationships are exactly equivalent.
This project was developed by Matthew Pennell, Rich FitzJohn, and Will Cornwell.
More information about the method is available in Pennell et al. 2016 Methods in Ecology and Evolution or on github.
You can install the github version of phyndr using devtools
install.packages("devtools")
devtools::install_github("traitecoevo/phyndr")
Or you can install from source on CRAN
install.packages("phyndr",type="source")