Rphylopars offers a variety of tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Available functions allow ancestral state reconstruction, missing data imputation, phylogenetic regression (phylogenetic generalized least squares), and phylogenetic principal components analysis (pPCA).
To get the most recent version of Rphylopars, run the following code in R:
require(devtools)
install_github("ericgoolsby/Rphylopars",ref = "devel",dependencies = TRUE)
# Un-comment and run the following if the above code doesn't work
# library(RCurl)
# library(httr)
# set_config( config( ssl_verifypeer = 0L ) )
# install_github("ericgoolsby/Rphylopars",ref = "devel",dependencies = TRUE)
Publications:
Goolsby EW, Bruggeman J, Ané C. "Rphylopars: an R package for Phylogenetic Comparative Methods for Missing Data and Within-Species Variation." In review.
Bruggeman J, Heringa J, Brandt BW. 2009. "PhyloPars: estimation of missing parameter values using phylogeny." Nucleic Acids Research. 37: W179-W184. [PDF]
Additionally, PhyloPars can be run using the PhyloPars Web interface described in Bruggeman et al. (2009).