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diversitree (version 0.7-2)

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. 69: 619), and GeoSSE (Geographic State Speciation and Extinction; Goldberg et al. 2011: 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

898

Version

0.7-2

License

GPL (>= 2)

Maintainer

Richard FitzJohn

Last Published

May 13th, 2011

Functions in diversitree (0.7-2)

constrain

Constrain Parameters of a Model
make.musse.td

Multiple State Speciation and Extinction Model: Time Dependent Models
make.bm

Brownian Motion Character Evolution
make.mkn.deriv

Mk2 and Mk-n Models of character evolution [temporary extension with derivatives]
asr-mkn

Ancestral State Reconstruction Under Mk2/Mkn
protect

Protect Function Evaluations
make.bd

Constant Rate Birth-Death Models
make.bd.t

Time-varing Birth-Death Models
make.clade.tree

Make a "Clade Tree"
simulate

Evolve Birth-Death Trees
asr

Ancestral State Reconstruction
asr-bisse

Ancestral State Reconstruction Under BiSSE
make.quasse.split

Quantitative State Speciation and Extinction Model: Split Models
make.musse

MuSSE: Multi-State Speciation and Extinction
make.bisse.td

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

Constant Rate Birth-Death Models: Split Models
plot.history

Plot Character History
profiles.plot

Plot Marginal Distributions from MCMC
big.brother

Verbosely Track Function Evaluations
Constants

Constants Used by Diversitree
make.mkn

Mk2 and Mk-n Models of character evolution
quasse-common

Support Functions for QuaSSE Models
mcmc

Simple Markov Chain Monte Carlo with Slice Sampling
geosse.phy

Example GeoSSE Tree
diversitree-deprecated

Deprecated and Defunct Functions in Diversitree
make.geosse

Geographic State Speciation and Extinction Model
time

Support Functions for Time-varying Models
history.from.sim

Extract Character Histories From Simulations
make.quasse

Quantitative State Speciation and Extinction Model
make.bisse.split

Binary State Speciation and Extinction Model: Split Models
argnames

Argument Names for Vector-Argument Functions
find.mle

Maximimum Likelihood Inference
make.bisse

Binary State Speciation and Extinction Model
make.musse.split

Multiple State Speciation and Extinction Model: Split Models
make.prior

Simple Prior Functions