Package: diversitree 0.10-1

Richard G. FitzJohn

diversitree: Comparative 'Phylogenetic' Analyses of Diversification

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.

Authors:Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen Magnuson-Ford [aut], Roger Sidje [aut]

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diversitree.pdf |diversitree.html✨
diversitree/json (API)

# Install 'diversitree' in R:
install.packages('diversitree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/richfitz/diversitree/issues

Uses libs:
  • fftw3– Library for computing Fast Fourier Transforms
  • gsl– GNU Scientific Library (GSL)
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

fftw3gslopenblascpp

9.10 score 30 stars 4 packages 502 scripts 1.1k downloads 33 mentions 101 exports 7 dependencies

Last updated 3 months agofrom:1687f0538c. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-win-x86_64OKDec 01 2024
R-4.5-linux-x86_64OKDec 01 2024
R-4.4-win-x86_64OKDec 01 2024
R-4.4-mac-x86_64OKDec 01 2024
R-4.4-mac-aarch64OKDec 01 2024
R-4.3-win-x86_64OKDec 01 2024
R-4.3-mac-x86_64OKDec 01 2024
R-4.3-mac-aarch64OKDec 01 2024

Exports:argnamesargnames<-asr.jointasr.marginalasr.stochbig.brothercheck.fftCclades.from.classificationclades.from.polytomiescombineconstant.xconstrainconstrain.idrop.likelihoodexpand.parametersfind.mleget.descendantsget.likelihoodhistory.from.sim.discreteinvertmake.asr.jointmake.asr.marginalmake.asr.stochmake.bdmake.bd.splitmake.bd.tmake.bissemake.bisse.splitmake.bisse.tmake.bisse.tdmake.bisse.unevenmake.bissenessmake.bmmake.brownian.with.driftmake.clade.treemake.classemake.ebmake.geossemake.geosse.splitmake.geosse.tmake.geosse.unevenmake.lambdamake.linear.xmake.mk2make.mknmake.mkn.meristicmake.mkn.multitraitmake.mussemake.musse.multitraitmake.musse.splitmake.musse.tmake.musse.tdmake.oumake.pglsmake.prior.exponentialmake.prior.uniformmake.quassemake.quasse.splitmake.sim.charactermake.yulemcmcmkn.multitrait.translatemusse.multitrait.translatenoroptimal.xpolytomies.to.cladesprofiles.plotprotectpruneROOT.ALLROOT.BOTHROOT.EQUIROOT.FLATROOT.GIVENROOT.MAXROOT.OBSrun.cachedsampler.normsampler.sliceset.defaultssigmoid.xsigmoid2.xsim.characterstarting.point.bdstarting.point.bissestarting.point.classestarting.point.geossestarting.point.mussestarting.point.musse.multitraitstarting.point.quassestepf.xtrait.plottree.bdtree.bissetree.bissenesstree.classetree.geossetree.mussetree.musse.multitraittree.quassetree.yuletrees

Dependencies:apedeSolvedigestlatticenlmeRcppsubplex

Readme and manuals

Help Manual

Help pageTopics
Comparative 'Phylogenetic' Analyses of Diversificationdiversitree-package diversitree
Argument Names for Vector-Argument Functionsargnames argnames.constrained argnames<- argnames<-.constrained
Ancestral State Reconstructionasr asr.joint asr.marginal asr.stoch make.asr.joint make.asr.marginal make.asr.stoch
Ancestral State Reconstruction Under BiSSEasr.bisse asr.marginal.bisse asr.marginal.musse asr.musse make.asr.marginal.bisse make.asr.marginal.musse
Ancestral State Reconstruction Under Mk2/Mknasr.mkn make.asr.joint.mk2 make.asr.joint.mkn make.asr.marginal.mk2 make.asr.marginal.mkn make.asr.stoch.mk2 make.asr.stoch.mkn
Check Capabilities of the Diversitree Installcheck.fftC
Combine Several Likelihood Functions Multiplicativelycombine
Constrain Parameters of a Modelconstrain constrain.i
Maximimum Likelihood Inferenceanova.fit.mle coef.fit.mle find.mle logLik.fit.mle
Extract Character Histories From Simulationshistory.from.sim.discrete
Constant Rate Birth-Death Modelsmake.bd make.yule starting.point.bd
Constant Rate Birth-Death Models: Split Modelsmake.bd.split
Time-varing Birth-Death Modelsmake.bd.t
Binary State Speciation and Extinction Modelmake.bisse starting.point.bisse
Binary State Speciation and Extinction Model: Split Modelsmake.bisse.split make.bisse.uneven
Binary State Speciation and Extinction Model: Time Dependant Modelsmake.bisse.t make.bisse.td
Binary State Speciation and Extinction (Node Enhanced State Shift) Modelmake.bisseness
Brownian Motion and Related Models of Character Evolutionmake.bm make.eb make.lambda make.ou
Make a "Clade Tree"clades.from.classification clades.from.polytomies make.clade.tree
Cladogenetic State change Speciation and Extinction Modelmake.classe starting.point.classe
Geographic State Speciation and Extinction Modelmake.geosse starting.point.geosse
Geographic State Speciation and Extinction Model: Split Modelsmake.geosse.split make.geosse.uneven
Geographic State Speciation and Extinction Model: Time Dependent Modelsmake.geosse.t
Mk2 and Mk-n Models of character evolutionmake.mk2 make.mkn make.mkn.meristic
MuSSE: Multi-State Speciation and Extinctionmake.musse starting.point.musse
MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)make.mkn.multitrait make.musse.multitrait mkn.multitrait.translate musse.multitrait.translate starting.point.musse.multitrait
Multiple State Speciation and Extinction Model: Split Modelsmake.musse.split
Multiple State Speciation and Extinction Model: Time Dependent Modelsmake.musse.t make.musse.td
Phylogenetic Generalised Least Squaresmake.pgls
Simple Prior Functionsmake.prior make.prior.exponential make.prior.uniform
Quantitative State Speciation and Extinction Modelmake.quasse starting.point.quasse
Quantitative State Speciation and Extinction Model: Split Modelsmake.quasse.split
Simple Markov Chain Monte Carlo with Slice Samplingmcmc mcmc.default sampler.norm sampler.slice
Plot Character Historyplot.history
Plot Marginal Distributions from MCMCprofiles.plot
Support Functions for QuaSSE Modelsconstant.x make.brownian.with.drift make.linear.x noroptimal.x sigmoid.x sigmoid2.x stepf.x
Set Default Arguments of a Functionset.defaults
Simulate a Character Distribution on a Treemake.sim.character sim.character
Evolve Birth-Death Treesprune tree.bd tree.bisse tree.bisseness tree.classe tree.geosse tree.musse tree.musse.multitrait tree.quasse tree.yule trees
Plot a Phylogeny and Traitstrait.plot
Utility Functionsdrop.likelihood expand.parameters get.descendants get.likelihood run.cached