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because.phybase

Phylogenetic Bayesian Structural Equation Models (PhyBaSE) extension for ‘because’

because.phybase extends the because package with support for phylogenetic covariance structures. It implements S3 methods for phylo and multiPhylo objects from the ape package, enabling Bayesian Structural Equation Models with phylogeneticaly-structured residuals (PhyBaSE, von Hardenberg & Gonzalez-Voyer, 2025).

Features

  • Phylogenetic Covariance: Incorporates phylogenetic relatedness into because models.
  • Phylogenetic Uncertainty: Supports multiPhylo objects to account for uncertainty in tree topology or branch lengths.
  • Measurement error: Accounting for measurement error in traits both providing repeated measures as well as specifying known measurement error variances.
  • Phylogenetic missing data imputation: informs imputation of missing data using phylogenetic relationships.
  • Seamless Integration: Designed to work transparently with because via S3 method dispatch.

Installation

To install because.phybase, run:

remotes::install_github("because-pkg/because.phybase")

because.phybase depends on because which will be installed automatically as a dependency. For information on the functions available in the main because package and for tutorials on how to fully use all its functionalities please refer to the because documentation