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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.

Functions (45)

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

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.bisse.split

Binary State Speciation and Extinction Model: Split Models

make.bisse.td

Binary State Speciation and Extinction Model: Time Dependant Models

make.bisseness

Binary State Speciation and Extinction (Node Enhanced State Shift) Model

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 Models

make.geosse.t

Geographic State Speciation and Extinction Model: Time Dependent Models

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 Traits Version)

make.musse.split

Multiple State Speciation and Extinction Model: Split Models

make.musse.td

Multiple State Speciation and Extinction Model: Time Dependent Models

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 Models

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

diversitree

Comparative 'Phylogenetic' Analyses of Diversification

v0.9-15

GPL (>= 2)

Authors

Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen Magnuson-Ford [aut], Roger Sidje [aut]

Initial release

diversitree

Functions (45)

diversitree

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