Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.


Rphylopars is an R package for conducting multivariate phylogenetic comparative analyses on datasets with missing observations and missing data. Rphylopars uses a fast linear-time algorithm and incorporate a variety of evolutionary models, including estimation of tree transformation parameters (Early-Burst, Ornstein-Uhlenbeck, lambda, kappa, delta) as well as the multivariate Ornstein-Uhlenbeck model.

For download information and tutorials, visit the Rphylopars wiki.

Current versions available

CRAN: 0.2.1

GitHub:

  • master branch - 0.2.3
  • devel branch - 0.2.3

Version notes

  • Version 0.2.2 - patch to allow a given species to have no data (previously this caused an error)
  • Version 0.2.3 - patch to retain node labels (if they exist) in ancestral state reconstruction

News

Reference manual

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install.packages("Rphylopars")

0.2.9 by Eric W. Goolsby, 3 years ago


http://github.com/ericgoolsby/Rphylopars/wiki


Browse source code at https://github.com/cran/Rphylopars


Authors: Eric W. Goolsby , Jorn Bruggeman , Cecile Ane


Documentation:   PDF Manual  


Task views: Missing Data


GPL (>= 2) license


Imports Rcpp, doBy, geiger, phylolm, phytools, mvnmle, Matrix, MASS

Depends on ape

Linking to Rcpp, RcppArmadillo


Suggested by PhylogeneticEM.


See at CRAN