Package index • diversitree

All functions
`argnames()` `argnames<-`()	Argument Names for Vector-Argument Functions
`make.asr.marginal(<bisse>)` `make.asr.marginal(<musse>)`	Ancestral State Reconstruction Under BiSSE
`make.asr.marginal(<mkn>)` `make.asr.joint(<mkn>)` `make.asr.stoch(<mkn>)`	Ancestral State Reconstruction Under Mk2/Mkn
`asr.marginal()` `asr.joint()` `asr.stoch()` `make.asr.marginal()` `make.asr.joint()` `make.asr.stoch()`	Ancestral State Reconstruction
`check.fftC()`	Check Capabilities of the Diversitree Install
`combine()`	Combine Several Likelihood Functions Multiplicatively
`constrain()` `constrain.i()`	Constrain Parameters of a Model
`diversitree-package` `diversitree`	Comparative 'Phylogenetic' Analyses of Diversification
`find.mle()` `coef(<fit.mle>)` `logLik(<fit.mle>)` `anova(<fit.mle>)`	Maximimum Likelihood Inference
`history.from.sim.discrete()`	Extract Character Histories From Simulations
`make.bd()` `make.yule()` `starting.point.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()` `starting.point.bisse()`	Binary State Speciation and Extinction Model
`make.bisse.split()` `make.bisse.uneven()`	Binary State Speciation and Extinction Model: Split Models
`make.bisse.td()` `make.bisse.t()`	Binary State Speciation and Extinction Model: Time Dependant Models
`make.bisseness()`	Binary State Speciation and Extinction (Node Enhanced State Shift) Model
`make.bm()` `make.ou()` `make.eb()` `make.lambda()`	Brownian Motion and Related Models of Character Evolution
`make.clade.tree()` `clades.from.polytomies()` `clades.from.classification()`	Make a "Clade Tree"
`make.classe()` `starting.point.classe()`	Cladogenetic State change Speciation and Extinction Model
`make.geosse()` `starting.point.geosse()`	Geographic State Speciation and Extinction Model
`make.geosse.split()` `make.geosse.uneven()`	Geographic State Speciation and Extinction Model: Split Models
`make.geosse.t()`	Geographic State Speciation and Extinction Model: Time Dependent Models
`make.mk2()` `make.mkn()` `make.mkn.meristic()`	Mk2 and Mk-n Models of character evolution
`make.musse()` `starting.point.musse()`	MuSSE: Multi-State Speciation and Extinction
`make.musse.multitrait()` `make.mkn.multitrait()` `musse.multitrait.translate()` `mkn.multitrait.translate()` `starting.point.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.td()` `make.musse.t()`	Multiple State Speciation and Extinction Model: Time Dependent Models
`make.pgls()`	Phylogenetic Generalised Least Squares
`make.prior.exponential()` `make.prior.uniform()`	Simple Prior Functions
`make.quasse()` `starting.point.quasse()`	Quantitative State Speciation and Extinction Model
`make.quasse.split()`	Quantitative State Speciation and Extinction Model: Split Models
`mcmc()` `sampler.slice()` `sampler.norm()`	Simple Markov Chain Monte Carlo with Slice Sampling
`plot(<history>)`	Plot Character History
`profiles.plot()`	Plot Marginal Distributions from MCMC
`constant.x()` `sigmoid.x()` `stepf.x()` `noroptimal.x()` `make.linear.x()` `make.brownian.with.drift()`	Support Functions for QuaSSE Models
`set.defaults()`	Set Default Arguments of a Function
`sim.character()` `make.sim.character()`	Simulate a Character Distribution on a Tree
`trees()` `tree.bisse()` `tree.musse()` `tree.musse.multitrait()` `tree.quasse()` `tree.bisseness()` `tree.classe()` `tree.geosse()` `tree.bd()` `tree.yule()` `prune()`	Evolve Birth-Death Trees
`trait.plot()`	Plot a Phylogeny and Traits
`get.descendants()` `run.cached()` `expand.parameters()` `get.likelihood()` `drop.likelihood()`	Utility Functions

Reference

All functions