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diversitree (version 0.9-6)

diversitree: comparative phylogenetic analyses of diversification

Description

Contains a number of comparative phylogenetic methods, mostly focusing 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. 59: 619), GeoSSE (Geographic State Speciation and Extinction; Goldberg et al. 2011: Syst. Biol. 60: 451), and BiSSE-ness (Magnuson-Ford and Otto 2012: Am. Nat.) 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

0.9-6

License

GPL (>= 2)

Maintainer

Rich FitzJohn

Last Published

June 13th, 2013

Functions in diversitree (0.9-6)

big.brother

Verbosely Track Function Evaluations
mcmc

Simple Markov Chain Monte Carlo with Slice Sampling
make.bm

Brownian Motion and Ornstein-Uhlenbeck Character Evolution
make.bisse.split

Binary State Speciation and Extinction Model: Split Models
plot.history

Plot Character History
make.bd.t

Time-varing Birth-Death Models
combine

Combine Several Likelihood Functions Multiplicatively
make.classe

Cladogenetic State change Speciation and Extinction Model
make.mkn

Mk2 and Mk-n Models of character evolution
history.from.sim

Extract Character Histories From Simulations
make.geosse

Geographic State Speciation and Extinction Model
make.prior

Simple Prior Functions
utilities

Utility Functions
quasse-common

Support Functions for QuaSSE Models
make.clade.tree

Make a "Clade Tree"
make.bisse

Binary State Speciation and Extinction Model
trait.plot

Plot a Phylogeny and Traits
make.bisseness

Binary State Speciation and Extinction (Node Enhanced State Shift) Model
make.geosse.split

Geographic State Speciation and Extinction Model: Split Models
make.quasse.split

Quantitative State Speciation and Extinction Model: Split Models
protect

Protect Function Evaluations
find.mle

Maximimum Likelihood Inference
constrain

Constrain Parameters of a Model
make.bd.split

Constant Rate Birth-Death Models: Split Models
argnames

Argument Names for Vector-Argument Functions
make.musse

MuSSE: Multi-State Speciation and Extinction
make.musse.multitrait

MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.bd

Constant Rate Birth-Death Models
geosse.phy

Example GeoSSE Tree
profiles.plot

Plot Marginal Distributions from MCMC
make.quasse

Quantitative State Speciation and Extinction Model
check

Check Capabilities of the Diversitree Install
Constants

Constants Used by Diversitree
set.defaults

Set Default Arguments of a Function
diversitree-deprecated

Deprecated and Defunct Functions in Diversitree
make.musse.td

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

Binary State Speciation and Extinction Model: Time Dependant Models
asr-bisse

Ancestral State Reconstruction Under BiSSE
make.musse.split

Multiple State Speciation and Extinction Model: Split Models
asr

Ancestral State Reconstruction
asr-mkn

Ancestral State Reconstruction Under Mk2/Mkn
simulate

Evolve Birth-Death Trees
sim.character

Simulate a Character Distribution on a Tree