paleotree: an R package for paleontological and phylogenetic analyses of evolution

Abstract

Summary 1. paleotree is a library of functions for the R statistical computing environment dedicated to analyses that combine paleontological and phylogenetic data sets, particularly the time‐scaling of phylogenetic trees, which include extinct fossil lineages. 2. The functions included in this library focus on simulating paleontological data sets, measuring sampling rates, time‐scaling cladograms of fossil taxa and plotting historical diversity curves. 3. I describe the capabilities and analytical basis of the functions in paleotree by presenting two examples. The first example showcases the simulation capabilities and plotting the output as diversity curves. The second example demonstrates time‐scaling a cladogram of fossil taxa and estimating sampling rates and completeness from temporal ranges.