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.

Author
Richard 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 publication
2016-10-05 11:30:53
Maintainer
Richard G. FitzJohn <rich.fitzjohn@gmail.com>
License
GPL (>= 2)
Version
0.9-9
URLs

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
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("diversitree")}
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