diversitree

MaRDI QIDQ37854swMATHCRANFDO

Authors Roger Sidje, Richard G. Fitzjohn, Karen Magnuson-Ford, Emma Goldberg

Last update 20 December 2023

Copyright license GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier 0.9-16, 0.9-18, 0.6-2, 0.6-3, 0.6-5, 0.7-2, 0.9-1, 0.9-3, 0.9-5, 0.9-6, 0.9-7, 0.9-8, 0.9-9, 0.9-10, 0.9-11, 0.9-13, 0.9-14, 0.9-15, 0.9-19, 0.9-20, 0.10-0

Official website https://cran.r-project.org/web/packages/diversitree/index.html

Source code repository https://github.com/cran/diversitree

Description

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

Cited in

(20)

• Efficient Bayesian inference of general Gaussian models on large phylogenetic trees
• Linking micro and macroevolution in the presence of migration
• The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
• phytools
• BEAUti
• GEIGER
• mvMORPH
• PCMBase
• Rphylopars
• apTreeshape
• logKDE
• ratematrix
• SPLITT
• ggtree
• treeio
• hisse
• HCTDesign
• Using multitype branching models to analyze bacterial pathogenicity
• Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts
• Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree

This page was built for software: diversitree