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.

AuthorRichard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE' and 'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by Karen Magnuson-Ford.
Date of publication2016-10-05 11:30:53
MaintainerRichard G. FitzJohn <rich.fitzjohn@gmail.com>
LicenseGPL (>= 2)
Version0.9-9
http://www.zoology.ubc.ca/prog/diversitree

View on CRAN

Man pages

argnames: Argument Names for Vector-Argument Functions

asr: Ancestral State Reconstruction

asr-bisse: Ancestral State Reconstruction Under BiSSE

asr-mkn: Ancestral State Reconstruction Under Mk2/Mkn

big.brother: Verbosely Track Function Evaluations

check: Check Capabilities of the Diversitree Install

combine: Combine Several Likelihood Functions Multiplicatively

constants: Constants Used by Diversitree

constrain: Constrain Parameters of a Model

diversitree-deprecated: Deprecated and Defunct Functions in Diversitree

diversitree-package: Comparative 'Phylogenetic' Analyses of Diversification

find.mle: Maximimum Likelihood Inference

geosse.phy: Example GeoSSE Tree

history.from.sim: Extract Character Histories From Simulations

make.bd: Constant Rate Birth-Death Models

make.bd.split: Constant Rate Birth-Death Models: Split Models

make.bd.t: Time-varing Birth-Death Models

make.bisse: Binary State Speciation and Extinction Model

make.bisseness: Binary State Speciation and Extinction (Node Enhanced State...

make.bisse.split: Binary State Speciation and Extinction Model: Split Models

make.bisse.td: Binary State Speciation and Extinction Model: Time Dependant...

make.bm: Brownian Motion and Related Models of Character Evolution

make.clade.tree: Make a "Clade Tree"

make.classe: Cladogenetic State change Speciation and Extinction Model

make.geosse: Geographic State Speciation and Extinction Model

make.geosse.split: Geographic State Speciation and Extinction Model: Split...

make.geosse.t: Geographic State Speciation and Extinction Model: Time...

make.mkn: Mk2 and Mk-n Models of character evolution

make.musse: MuSSE: Multi-State Speciation and Extinction

make.musse.multitrait: MuSSE: Multi-State Speciation and Extinction (Multiple Binary...

make.musse.split: Multiple State Speciation and Extinction Model: Split Models

make.musse.td: Multiple State Speciation and Extinction Model: Time...

make.pgls: Phylogenetic Generalised Least Squares

make.prior: Simple Prior Functions

make.quasse: Quantitative State Speciation and Extinction Model

make.quasse.split: Quantitative State Speciation and Extinction Model: Split...

mcmc: Simple Markov Chain Monte Carlo with Slice Sampling

plot.history: Plot Character History

profiles.plot: Plot Marginal Distributions from MCMC

protect: Protect Function Evaluations

quasse-common: Support Functions for QuaSSE Models

set.defaults: Set Default Arguments of a Function

sim.character: Simulate a Character Distribution on a Tree

simulate: Evolve Birth-Death Trees

trait.plot: Plot a Phylogeny and Traits

utils: Utility Functions

Files in this package

diversitree
diversitree/TODO
diversitree/inst
diversitree/inst/CITATION
diversitree/inst/tests
diversitree/inst/tests/test-utils.R
diversitree/inst/tests/bisse-tree.ttn
diversitree/inst/tests/test-bisseness.R
diversitree/inst/tests/geosse-tree.ttn
diversitree/inst/tests/test-time-machine.R
diversitree/inst/tests/test-expm.R
diversitree/inst/tests/test-bd.R
diversitree/inst/tests/run-tests.R
diversitree/inst/tests/test-quasse.R
diversitree/inst/tests/test-mle.R
diversitree/inst/tests/phy.Rdata
diversitree/inst/tests/test-bd-t.R
diversitree/inst/tests/test-quasse-split.R
diversitree/inst/tests/test-ou.R
diversitree/inst/tests/test-classe.R
diversitree/inst/tests/test-bisse.R
diversitree/inst/tests/test-musse-t.R
diversitree/inst/tests/helper-diversitree.R
diversitree/inst/tests/test-mcmc.R
diversitree/inst/tests/test-bisse-td.R
diversitree/inst/tests/test-bm.R
diversitree/inst/tests/classe-tree.ttn
diversitree/inst/tests/test-unresolved.R
diversitree/inst/tests/test-eb.R
diversitree/inst/tests/test-quasse-internal.R
diversitree/inst/tests/test-musse-split.R
diversitree/inst/tests/test-bisse-split.R
diversitree/inst/tests/test-ode.R
diversitree/inst/tests/test-geosse.R
diversitree/inst/tests/test-pgls.R
diversitree/inst/tests/test-lambda.R
diversitree/inst/tests/test-mkn.R
diversitree/inst/tests/test-musse.R
diversitree/inst/tests/test-musse-multitrait.R
diversitree/inst/tests/test-asr-t.R
diversitree/inst/tests/test-rescale.R
diversitree/inst/tests/test-asr.R
diversitree/inst/tests/test-geosse-t.R
diversitree/inst/tests/test-branches.R
diversitree/inst/tests/test-bisse-t.R
diversitree/inst/tests/test-bd-split.R
diversitree/inst/CONTRIBUTORS.md
diversitree/inst/update-gh-pages.sh
diversitree/configure.ac
diversitree/src
diversitree/src/GslOdeBase.cpp
diversitree/src/util.c
diversitree/src/GslOdeTime.cpp
diversitree/src/GslOdeBase.h
diversitree/src/geosse-eqs.c
diversitree/src/dmexpv.f
diversitree/src/config.h.win
diversitree/src/mkn-pij.h
diversitree/src/GslOdeR.cpp
diversitree/src/mkn-expokit.h
diversitree/src/hdr.c
diversitree/src/config.h.in
diversitree/src/scm-mkn.h
diversitree/src/bisseness-eqs.c
diversitree/src/hyperg.f
diversitree/src/rfftw.h
diversitree/src/mkn-pij.c
diversitree/src/util-splines.h
diversitree/src/hdr.h
diversitree/src/bd-eqs.c
diversitree/src/mkn-expokit.c
diversitree/src/GslOdeTime.h
diversitree/src/dsexpv.f
diversitree/src/Spline.h
diversitree/src/asr-joint.c
diversitree/src/util-matrix.c
diversitree/src/dgpadm.f
diversitree/src/quasse-eqs-fftC.c
diversitree/src/continuous.h
diversitree/src/GslOdeCompiled.cpp
diversitree/src/derivs.c
diversitree/src/TimeMachine.cpp
diversitree/src/continuous.c
diversitree/src/util.h
diversitree/src/dsexpvi.f
diversitree/src/Makevars.in
diversitree/src/dgcoov.f
diversitree/src/Spline.cpp
diversitree/src/musse-eqs.c
diversitree/src/expm.f
diversitree/src/mkn-eqs.c
diversitree/src/quasse-eqs-mol.c
diversitree/src/dnchbv.f
diversitree/src/simulate-bisse.c
diversitree/src/util-matrix.h
diversitree/src/classe-eqs.c
diversitree/src/GslOdeR.h
diversitree/src/bisse-eqs.c
diversitree/src/scm-mkn.c
diversitree/src/Makevars.win
diversitree/src/interface.cpp
diversitree/src/nucexp.f
diversitree/src/rfftw.c
diversitree/src/GslOdeCompiled.h
diversitree/src/dgexpvi.f
diversitree/src/quasse-eqs-fftC.h
diversitree/src/TimeMachine.h
diversitree/src/util-splines.c
diversitree/src/bucexp.f
diversitree/src/mkn-meristic-eqs.c
diversitree/src/derivs.h
diversitree/NAMESPACE
diversitree/R
diversitree/R/model-bm.R diversitree/R/mle-subplexR.R diversitree/R/gslode.R diversitree/R/mcmc-norm.R diversitree/R/model-bisseness.R diversitree/R/model-musse-td.R diversitree/R/simulate-quasse.R diversitree/R/model-mkn-meristic.R diversitree/R/model-bm-vcv.R diversitree/R/model-mkn-multitrait.R diversitree/R/model-quasse-fftC.R diversitree/R/model-lambda.R diversitree/R/model-bd-t.R diversitree/R/model-geosse-t.R diversitree/R/simulate-musse.R diversitree/R/model-bm-contrasts.R diversitree/R/check.R diversitree/R/model-musse.R diversitree/R/model-classe.R diversitree/R/sim-character.R diversitree/R/model-eb.R diversitree/R/asr-mkn.R diversitree/R/model-musse-t.R diversitree/R/desolve.R diversitree/R/clade-tree.R diversitree/R/mcmc-hmc.R diversitree/R/model-bisse-td.R diversitree/R/history.R diversitree/R/mle-integer.R diversitree/R/drop.tip.fixed.R diversitree/R/model-geosse.R diversitree/R/model-bd-ode.R diversitree/R/model-ou.R diversitree/R/model-bd.R diversitree/R/model-bd-nee.R diversitree/R/model-quasse-fftR.R diversitree/R/rescale.R diversitree/R/simulate-bd.R diversitree/R/simulate-geosse.R diversitree/R/model-musse-split.R diversitree/R/mle.R diversitree/R/mle-mixed.R diversitree/R/asr-musse.R diversitree/R/plot-alt.R diversitree/R/simulation.R diversitree/R/model-pgls.R diversitree/R/model-bm-pruning.R diversitree/R/td.R diversitree/R/t.R diversitree/R/mle-optimize.R diversitree/R/model-quasse-split.R diversitree/R/model-quasse-mol.R diversitree/R/model-musse-multitrait.R diversitree/R/model-bisse-unresolved.R diversitree/R/simulate-classe.R diversitree/R/util-tree.R diversitree/R/model-quasse-common.R diversitree/R/mle-grid.R diversitree/R/asr-bisse.R diversitree/R/model-bisse-split.R diversitree/R/model-bd-split.R diversitree/R/model-mkn-expokit.R diversitree/R/continuous.R diversitree/R/model-mkn.R diversitree/R/asr.R diversitree/R/constrain.R diversitree/R/model-geosse-split.R diversitree/R/dtlik.R diversitree/R/split.R diversitree/R/util.R diversitree/R/model-ou-pruning.R diversitree/R/mcmc-slice.R diversitree/R/model-bisse-t.R diversitree/R/simulate-bisseness.R diversitree/R/model-bisseness-unresolved.R diversitree/R/profiles-plot.R diversitree/R/asr-t.R diversitree/R/time-machine.R diversitree/R/mle-methods.R diversitree/R/mcmc.R diversitree/R/plot-alt-util.R diversitree/R/model-quasse.R diversitree/R/model-mkn-pij.R diversitree/R/expm.R diversitree/R/zzz.R diversitree/R/plot-alt-extra.R diversitree/R/diversitree-branches.R diversitree/R/model-bisse.R diversitree/R/simulate-bisse.R diversitree/R/asr-geosse.R diversitree/R/model-mkn-ode.R
diversitree/README.md
diversitree/MD5
diversitree/build
diversitree/build/partial.rdb
diversitree/DESCRIPTION
diversitree/configure
diversitree/ChangeLog
diversitree/man
diversitree/man/constants.Rd diversitree/man/profiles.plot.Rd diversitree/man/make.geosse.split.Rd diversitree/man/make.quasse.split.Rd diversitree/man/set.defaults.Rd diversitree/man/make.mkn.Rd diversitree/man/protect.Rd diversitree/man/trait.plot.Rd diversitree/man/simulate.Rd diversitree/man/combine.Rd diversitree/man/sim.character.Rd diversitree/man/make.prior.Rd diversitree/man/history.from.sim.Rd diversitree/man/big.brother.Rd diversitree/man/make.geosse.t.Rd diversitree/man/diversitree-deprecated.Rd diversitree/man/utils.Rd diversitree/man/quasse-common.Rd diversitree/man/constrain.Rd diversitree/man/asr.Rd diversitree/man/make.musse.split.Rd diversitree/man/make.bd.t.Rd diversitree/man/geosse.phy.Rd diversitree/man/make.bisse.Rd diversitree/man/make.bisse.td.Rd diversitree/man/make.pgls.Rd diversitree/man/asr-mkn.Rd diversitree/man/asr-bisse.Rd diversitree/man/diversitree-package.Rd diversitree/man/make.bisseness.Rd diversitree/man/make.musse.Rd diversitree/man/make.bd.Rd diversitree/man/make.quasse.Rd diversitree/man/make.bisse.split.Rd diversitree/man/make.geosse.Rd diversitree/man/find.mle.Rd diversitree/man/check.Rd diversitree/man/make.musse.multitrait.Rd diversitree/man/make.bm.Rd diversitree/man/make.classe.Rd diversitree/man/make.musse.td.Rd diversitree/man/plot.history.Rd diversitree/man/argnames.Rd diversitree/man/make.clade.tree.Rd diversitree/man/make.bd.split.Rd diversitree/man/mcmc.Rd
diversitree/configure.win
diversitree/cleanup

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