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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.