ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework

Abstract Understanding how changes in climate affect habitat availability for species through time is critical for macroevolutionary, ecological, and conservation research. When combined with palaeoclimate reconstructions, the fossil record provides insights into how species' geographic distributions have responded to past climate shifts, including under non‐analogous climate conditions. Palaeophylogeographic models (PPGMs) offer a framework to integrate modern and palaeontological data into phylogenetic comparative analyses of species climate tolerances. The ppgm R package is an implementation of PPGMs, which estimates species climate envelopes, reconstructs ancestral climatic tolerances across phylogenies, and projects these onto palaeoclimatic maps to identify climatically available regions through time. The package also supports direct inclusion of fossil occurrences with associated palaeoclimatic data, allowing a reconstruction of past trends of species climate tolerances projected into palaeoclimatic maps to pinpoint the locations of climate availability through time according to the fossil record. We demonstrate the broad applicability of ppgm through detailed case studies, showing its potential for addressing research questions in macroevolutionary and conservation palaeobiology research. The ppgm package complements existing R packages by allowing researchers to use analytical techniques on large integrated datasets and facilitates reproducible analyses of species climate niches over deep and shallow time.