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diversitree (version 0.6-3)

diversitree: comparative phylogenetic tests of diversification

Description

Contains a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution. Contains implementations of BiSSE (Binary State Speciation and Extinction; Maddison et al. 2007: Syst. Biol. 56: 701) and its unresolved tree extensions (FitzJohn et al. 2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation and Extinction), QuaSSE (Quantitative State Speciation and Extinction; FitzJohn 2010: Syst. Biol. in press), and GeoSSE (Geographic State Speciation and Extinction; Goldberg et al. 2010: Syst. Biol.). Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.

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Version

Install

install.packages('diversitree')

Monthly Downloads

714

Version

0.6-3

License

GPL (>= 2)

Maintainer

Richard FitzJohn

Last Published

January 27th, 2011

Functions in diversitree (0.6-3)

argnames

Argument Names for Vector-Argument Functions
geosse.phy

Example GeoSSE Tree
simulate

Evolve Birth-Death Trees
mcmc

Simple Markov Chain Monte Carlo with Slice Sampling
asr-mkn

Ancestral State Reconstruction Under Mk2/Mkn
make.bm

Brownian Motion Character Evolution
asr-bisse

Ancestral State Reconstruction Under BiSSE
make.quasse

Quantitative State Speciation and Extinction Model
make.musse

MuSSE: Multi-State Speciation and Extinction
quasse-common

Support Functions for QuaSSE Models
profiles.plot

Plot Marginal Distributions from MCMC
Constants

Constants Used by Diversitree
make.bd.split

Constant Rate Birth-Death Models: Split Models
make.clade.tree

Make a "Clade Tree"
history.from.sim

Extract Character Histories From Simulations
make.bd

Constant Rate Birth-Death Models
make.bd.t

Time-varing Birth-Death Models
make.quasse.split

Quantitative State Speciation and Extinction Model: Split Models
asr

Ancestral State Reconstruction
make.bisse.td

Binary State Speciation and Extinction Model: Time Dependant Models
make.musse.split

Multiple State Speciation and Extinction Model: Split Models
time

Support Functions for Time-varying Models
make.mkn

Mk2 and Mk-n Models of character evolution
make.bisse.split

Binary State Speciation and Extinction Model: Split Models
big.brother

Verbosely Track Function Evaluations
make.musse.td

Multiple State Speciation and Extinction Model: Time Dependent Models
plot.history

Plot Character History
diversitree-deprecated

Deprecated and Defunct Functions in Diversitree
make.geosse

Geographic State Speciation and Extinction Model
protect

Protect Function Evaluations
make.prior

Simple Prior Functions
find.mle

Maximimum Likelihood Inference
make.bisse

Binary State Speciation and Extinction Model
constrain

Constrain Parameters of a Model