Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST
Rieux, Adrien; Khatchikian, Camilo E. (2016), Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST, Dryad, Dataset, https://doi.org/10.5061/dryad.43q71
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation.