strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

Abstract

strap (S tratigraphic T ree A nalysis for P alaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time‐scale phylogenies of fossil taxa; (2) to plot those time‐scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time‐scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: S tratigraphic C onsistency I ndex (SCI), M anhattan S tratigraphic M easure (MSM*) and the gap excess ratio (GER; including GER t and GER*), as well as the pseudocongruence measure, the R elative C ompleteness I ndex (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user‐defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.