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 (Goolsby et al. 2017). 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


  • 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


Reference manual

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0.3.2 by Eric W. Goolsby, 8 months ago

Browse source code at

Authors: Eric W. Goolsby [aut, cre] , Jorn Bruggeman [aut] , Cecile Ane [aut]

Documentation:   PDF Manual  

Task views:

GPL (>= 2) license

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

Depends on ape

Linking to Rcpp, RcppArmadillo

See at CRAN