prepR4pcm: An R package for preparing data and trees for phylogenetic comparative methods

Abstract

Phylogenetic comparative methods require species names in a trait dataset to match tip labels in a phylogenetic tree. Yet this apparently simple prerequisite is often one of the most fragile steps in a comparative workflow. Names may differ because of, for example, formatting, taxonomic revisions, synonyms, or spelling errors. If these differences are resolved informally, species can be lost from analyses, and the reasons for their loss can be difficult to reconstruct. Here, we present