Phylogenetic Comparative Tools for Missing Data and Within-Species Variation.

Rphylopars

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: 0.3.9 (0.3.10 submission pending)

GitHub master branch - 0.3.10

GitHub devel branch - 0.3.10

Version notes

• Version 0.3.10 - Removed arma::set_cerr_stream() to address deprecation warning.
• Version 0.3.9 - Added get_cov_CIs as option to phylopars to estimate 95% confidence intervals for trait covariance parameters. Clean up write.phylopars() function Also removed dependency on geiger, which is set to be archived on CRAN.
• Version 0.3.8 - Fixes sim.traits() error which previously set root value to 1.
• Version 0.3.7 - Converts trait_data to data.frame to prevent errors from tibbles
• Version 0.3.6 - New experimental internal function Rphylopars:::get_cov_CIs to estimate 95% CIs for trait covariance parameters from a fitted phylopars object.
• Version 0.3.5 - Checks that all species names in trait_data$species have an exact match in tree$tip.label
• Version 0.3.4 - Fixes printing error when only one variable is included in phylopars()
• Version 0.3.3 - Prevents R from crashing when is.na(species) (e.g. trailing blank rows at the end of a spreadsheet).
• Version 0.3.1 and 0.3.2 - Removed broken links from fast.SSC.Rd and Rphylopars-package.Rd help files (resolves CRAN notes)
• Version 0.3.0 - R 4.0 compatibility
• Version 0.2.11 - Fixed confidence intervals (previously too large) and installation issues.