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.
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.sim.traits() error which previously set root value to 1.trait_data to data.frame to prevent errors from tibblesRphylopars:::get_cov_CIs to estimate 95% CIs for trait covariance parameters from a fitted phylopars object.trait_data$species have an exact match in tree$tip.labelphylopars()