title: iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees.
abstract: Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Fordyce
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA. ; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Premal
authors.initials: P
authors.lastname: Shah
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA. ; National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Fitzpatrick
keywords: chronogram; diversification-rate; phylogeny; rate-variation