Comparative 'Phylogenetic' Analyses of Diversification


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Documentation for package ‘diversitree’ version 0.9-15

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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