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

Functions

anova.fit.mle Man page
argnames Man page
argnames<- Man page
argnames<-.constrained Man page
argnames.constrained Man page
asr Man page
asr.bisse Man page
asr.joint Man page
asr.marginal Man page
asr.marginal.bisse Man page
asr.marginal.musse Man page
asr.mkn Man page
asr.musse Man page
asr.stoch Man page
big.brother Man page
check.fftC Man page
clades.from.classification Man page
clades.from.polytomies Man page
coef.fit.mle Man page
combine Man page
constant.x Man page
constrain Man page
constrain.i Man page
diversitree Man page
diversitree-deprecated Man page
diversitree-package Man page
drop.likelihood Man page
expand.parameters Man page
find.mle Man page
geosse.phy Man page
get.descendants Man page
get.likelihood Man page
history.from.sim.discrete Man page
invert Man page
logLik.fit.mle Man page
make.asr.joint Man page
make.asr.joint.mk2 Man page
make.asr.joint.mkn Man page
make.asr.marginal Man page
make.asr.marginal.bisse Man page
make.asr.marginal.mk2 Man page
make.asr.marginal.mkn Man page
make.asr.marginal.musse Man page
make.asr.stoch Man page
make.asr.stoch.mk2 Man page
make.asr.stoch.mkn Man page
make.bd Man page
make.bd.split Man page
make.bd.t Man page
make.bisse Man page
make.bisseness Man page
make.bisse.split Man page
make.bisse.t Man page
make.bisse.td Man page
make.bisse.uneven Man page
make.bm Man page
make.brownian.with.drift Man page
make.clade.tree Man page
make.classe Man page
make.eb Man page
make.geosse Man page
make.geosse.split Man page
make.geosse.t Man page
make.geosse.uneven Man page
make.lambda Man page
make.linear.x Man page
make.mk2 Man page
make.mkn Man page
make.mkn.meristic Man page
make.mkn.multitrait Man page
make.musse Man page
make.musse.multitrait Man page
make.musse.split Man page
make.musse.t Man page
make.musse.td Man page
make.ou Man page
make.pgls Man page
make.prior Man page
make.prior.exponential Man page
make.prior.uniform Man page
make.quasse Man page
make.quasse.split Man page
make.sim.character Man page
make.yule Man page
mcmc Man page
mcmc.default Man page
mkn.multitrait.translate Man page
musse.multitrait.translate Man page
noroptimal.x Man page
plot.history Man page
polytomies.to.clades Man page
profiles.plot Man page
protect Man page
prune Man page
ROOT.ALL Man page
ROOT.BOTH Man page
ROOT.EQUI Man page
ROOT.FLAT Man page
ROOT.GIVEN Man page
ROOT.MAX Man page
ROOT.OBS Man page
run.cached Man page
sampler.norm Man page
sampler.slice Man page
set.defaults Man page
sigmoid2.x Man page
sigmoid.x Man page
sim.character Man page
starting.point.bd Man page
starting.point.bisse Man page
starting.point.classe Man page
starting.point.geosse Man page
starting.point.musse Man page
starting.point.musse.multitrait Man page
starting.point.quasse Man page
stepf.x Man page
trait.plot Man page
tree.bd Man page
tree.bisse Man page
tree.bisseness Man page
tree.classe Man page
tree.geosse Man page
tree.musse Man page
tree.musse.multitrait Man page
tree.quasse Man page
trees Man page
tree.yule Man page

Files

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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