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diversitree  

Comparative 'Phylogenetic' Analyses of Diversification
View on CRAN: Click here


Download and install diversitree package within the R console
Install from CRAN:
install.packages("diversitree")

Install from Github:
library("remotes")
install_github("cran/diversitree")

Install by package version:
library("remotes")
install_version("diversitree", "0.10-1")



Attach the package and use:
library("diversitree")
Maintained by
Richard G. FitzJohn
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-12-16
Latest Update: 2024-10-02
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.
How to cite:
Richard G. FitzJohn (2010). diversitree: Comparative 'Phylogenetic' Analyses of Diversification. R package version 0.10-1, https://cran.r-project.org/web/packages/diversitree. Accessed 25 Jun. 2026.
Previous versions and publish date:
0.6-2 (2010-12-16 10:31), 0.6-3 (2011-01-27 11:33), 0.6-5 (2011-04-24 08:07), 0.7-2 (2011-05-13 08:58), 0.9-1 (2012-03-15 06:19), 0.9-3 (2012-05-08 06:06), 0.9-5 (2013-06-13 11:00), 0.9-6 (2013-06-13 16:15), 0.9-7 (2014-02-20 07:37), 0.9-8 (2015-12-21 16:27), 0.9-9 (2016-10-05 11:30), 0.9-10 (2017-04-05 13:15), 0.9-11 (2019-03-14 14:50), 0.9-13 (2020-01-16 14:20), 0.9-14 (2020-09-04 18:02), 0.9-15 (2020-11-24 15:50), 0.9-16 (2021-06-11 17:00), 0.9-18 (2023-05-03 12:40), 0.9-19 (2023-08-17 18:12), 0.9-20 (2023-09-06 11:10), 0.10-0 (2023-12-20 17:40)
Other packages that cited diversitree R package
View diversitree citation profile
Other R packages that diversitree depends, imports, suggests or enhances
Complete documentation for diversitree
Functions, R codes and Examples using the diversitree R package
Some associated functions: argnames . asr-bisse . asr-mkn . asr . big.brother . check . combine . constants . constrain . diversitree-deprecated . diversitree-package . find.mle . history.from.sim . make.bd . make.bd.split . make.bd.t . make.bisse . make.bisse.split . make.bisse.td . make.bisseness . make.bm . make.clade.tree . make.classe . make.geosse . make.geosse.split . make.geosse.t . make.mkn . make.musse.multitrait . make.musse . make.musse.split . make.musse.td . make.pgls . make.prior . make.quasse . make.quasse.split . mcmc . plot.history . profiles.plot . protect . quasse-common . set.defaults . sim.character . simulate . trait.plot . utils . 
Some associated R codes: asr-bisse.R . asr-geosse.R . asr-mkn.R . asr-musse.R . asr-t.R . asr.R . check.R . clade-tree.R . constrain.R . continuous.R . desolve.R . diversitree-branches.R . drop.tip.fixed.R . dtlik.R . expm.R . gslode.R . history.R . mcmc-hmc.R . mcmc-norm.R . mcmc-slice.R . mcmc.R . mle-grid.R . mle-integer.R . mle-methods.R . mle-mixed.R . mle-optimize.R . mle-subplexR.R . mle.R . model-bd-nee.R . model-bd-ode.R . model-bd-split.R . model-bd-t.R . model-bd.R . model-bisse-split.R . model-bisse-t.R . model-bisse-td.R . model-bisse-unresolved.R . model-bisse.R . model-bisseness-unresolved.R . model-bisseness.R . model-bm-contrasts.R . model-bm-pruning.R . model-bm-vcv.R . model-bm.R . model-classe.R . model-eb.R . model-geosse-split.R . model-geosse-t.R . model-geosse.R . model-lambda.R . model-mkn-meristic.R . model-mkn-multitrait.R . model-mkn-ode.R . model-mkn-pij.R . model-mkn.R . model-musse-multitrait.R . model-musse-split.R . model-musse-t.R . model-musse-td.R . model-musse.R . model-ou-pruning.R . model-ou.R . model-pgls.R . model-quasse-common.R . model-quasse-fftC.R . model-quasse-fftR.R . model-quasse-mol.R . model-quasse-split.R . model-quasse.R . plot-alt-extra.R . plot-alt-util.R . plot-alt.R . profiles-plot.R . rescale.R . sim-character.R . simulate-bd.R . simulate-bisse.R . simulate-bisseness.R . simulate-classe.R . simulate-geosse.R . simulate-musse.R . simulate-quasse.R . simulation.R . split.R . t.R . td.R . time-machine.R . util-tree.R . util.R . zzz.R .  Full diversitree package functions and examples
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