# Comparative 'Phylogenetic' Analyses of Diversification

## Documentation for package ‘diversitree’ version 0.9-13

- DESCRIPTION file.

## Help Pages

A C D E F G H L M N P R S T

diversitree-package | Comparative 'Phylogenetic' Analyses of Diversification

## -- A --

anova.fit.mle | Maximimum Likelihood Inference
argnames | Argument Names for Vector-Argument Functions
argnames.constrained | Argument Names for Vector-Argument Functions
argnames<- | Argument Names for Vector-Argument Functions
argnames<-.constrained | Argument Names for Vector-Argument Functions
asr | Ancestral State Reconstruction
asr.bisse | Ancestral State Reconstruction Under BiSSE
asr.joint | Ancestral State Reconstruction
asr.marginal | Ancestral State Reconstruction
asr.marginal.bisse | Ancestral State Reconstruction Under BiSSE
asr.marginal.musse | Ancestral State Reconstruction Under BiSSE
asr.mkn | Ancestral State Reconstruction Under Mk2/Mkn
asr.musse | Ancestral State Reconstruction Under BiSSE
asr.stoch | Ancestral State Reconstruction

## -- C --

check.fftC | Check Capabilities of the Diversitree Install
clades.from.classification | Make a "Clade Tree"
clades.from.polytomies | Make a "Clade Tree"
coef.fit.mle | Maximimum Likelihood Inference
combine | Combine Several Likelihood Functions Multiplicatively
constant.x | Support Functions for QuaSSE Models
constrain | Constrain Parameters of a Model
constrain.i | Constrain Parameters of a Model

## -- D --

diversitree | Comparative 'Phylogenetic' Analyses of Diversification
drop.likelihood | Utility Functions

## -- E --

expand.parameters | Utility Functions

## -- F --

find.mle | Maximimum Likelihood Inference

## -- G --

get.descendants | Utility Functions
get.likelihood | Utility Functions

## -- H --

history.from.sim.discrete | Extract Character Histories From Simulations

## -- L --

logLik.fit.mle | Maximimum Likelihood Inference

## -- M --

make.asr.joint | Ancestral State Reconstruction
make.asr.joint.mk2 | Ancestral State Reconstruction Under Mk2/Mkn
make.asr.joint.mkn | Ancestral State Reconstruction Under Mk2/Mkn
make.asr.marginal | Ancestral State Reconstruction
make.asr.marginal.bisse | Ancestral State Reconstruction Under BiSSE
make.asr.marginal.mk2 | Ancestral State Reconstruction Under Mk2/Mkn
make.asr.marginal.mkn | Ancestral State Reconstruction Under Mk2/Mkn
make.asr.marginal.musse | Ancestral State Reconstruction Under BiSSE
make.asr.stoch | Ancestral State Reconstruction
make.asr.stoch.mk2 | Ancestral State Reconstruction Under Mk2/Mkn
make.asr.stoch.mkn | Ancestral State Reconstruction Under Mk2/Mkn
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.bisse.split | Binary State Speciation and Extinction Model: Split Models
make.bisse.t | Binary State Speciation and Extinction Model: Time Dependant Models
make.bisse.td | Binary State Speciation and Extinction Model: Time Dependant Models
make.bisse.uneven | Binary State Speciation and Extinction Model: Split Models
make.bisseness | Binary State Speciation and Extinction (Node Enhanced State Shift) Model
make.bm | Brownian Motion and Related Models of Character Evolution
make.brownian.with.drift | Support Functions for QuaSSE Models
make.clade.tree | Make a "Clade Tree"
make.classe | Cladogenetic State change Speciation and Extinction Model
make.eb | Brownian Motion and Related Models of Character Evolution
make.geosse | Geographic State Speciation and Extinction Model
make.geosse.split | Geographic State Speciation and Extinction Model: Split Models
make.geosse.t | Geographic State Speciation and Extinction Model: Time Dependent Models
make.geosse.uneven | Geographic State Speciation and Extinction Model: Split Models
make.lambda | Brownian Motion and Related Models of Character Evolution
make.linear.x | Support Functions for QuaSSE Models
make.mk2 | Mk2 and Mk-n Models of character evolution
make.mkn | Mk2 and Mk-n Models of character evolution
make.mkn.meristic | Mk2 and Mk-n Models of character evolution
make.mkn.multitrait | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.musse | MuSSE: Multi-State Speciation and Extinction
make.musse.multitrait | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.musse.split | Multiple State Speciation and Extinction Model: Split Models
make.musse.t | Multiple State Speciation and Extinction Model: Time Dependent Models
make.musse.td | Multiple State Speciation and Extinction Model: Time Dependent Models
make.ou | Brownian Motion and Related Models of Character Evolution
make.pgls | Phylogenetic Generalised Least Squares
make.prior | Simple Prior Functions
make.prior.exponential | Simple Prior Functions
make.prior.uniform | Simple Prior Functions
make.quasse | Quantitative State Speciation and Extinction Model
make.quasse.split | Quantitative State Speciation and Extinction Model: Split Models
make.sim.character | Simulate a Character Distribution on a Tree
make.yule | Constant Rate Birth-Death Models
mcmc | Simple Markov Chain Monte Carlo with Slice Sampling
mcmc.default | Simple Markov Chain Monte Carlo with Slice Sampling
mkn.multitrait.translate | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
musse.multitrait.translate | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)

## -- N --

noroptimal.x | Support Functions for QuaSSE Models

## -- P --

plot.history | Plot Character History
profiles.plot | Plot Marginal Distributions from MCMC
prune | Evolve Birth-Death Trees

## -- R --

run.cached | Utility Functions

## -- S --

sampler.norm | Simple Markov Chain Monte Carlo with Slice Sampling
sampler.slice | Simple Markov Chain Monte Carlo with Slice Sampling
set.defaults | Set Default Arguments of a Function
sigmoid.x | Support Functions for QuaSSE Models
sigmoid2.x | Support Functions for QuaSSE Models
sim.character | Simulate a Character Distribution on a Tree
starting.point.bd | Constant Rate Birth-Death Models
starting.point.bisse | Binary State Speciation and Extinction Model
starting.point.classe | Cladogenetic State change Speciation and Extinction Model
starting.point.geosse | Geographic State Speciation and Extinction Model
starting.point.musse | MuSSE: Multi-State Speciation and Extinction
starting.point.musse.multitrait | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
starting.point.quasse | Quantitative State Speciation and Extinction Model
stepf.x | Support Functions for QuaSSE Models

## -- T --

trait.plot | Plot a Phylogeny and Traits
tree.bd | Evolve Birth-Death Trees
tree.bisse | Evolve Birth-Death Trees
tree.bisseness | Evolve Birth-Death Trees
tree.classe | Evolve Birth-Death Trees
tree.geosse | Evolve Birth-Death Trees
tree.musse | Evolve Birth-Death Trees
tree.musse.multitrait | Evolve Birth-Death Trees
tree.quasse | Evolve Birth-Death Trees
tree.yule | Evolve Birth-Death Trees
trees | Evolve Birth-Death Trees