title: tipdatingbeast: an r package to assist the implementation of phylogenetic tip-dating tests using beast.
abstract: Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate 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 data set. 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 data set and supply practical guidance for results interpretation.
authors.affiliation: CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Rieux
authors.affiliation: Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA, 19104, USA.|Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave, Bioscience Research Bldg. Room 2.120, EL Paso, TX, 79968, USA.
authors.forename: Camilo E
authors.initials: CE
authors.lastname: Khatchikian
mesh_terms: D001499:Bayes Theorem; D002138:Calibration; D019143:Evolution, Molecular; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software
keywords: 
  beast
  ; date-randomization test; leave-one-out cross-validation; measurably-evolving populations; phylogenetic tip-dating