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diversitree (version 0.9-5)

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

0.9-5

License

GPL (>= 2)

Maintainer

Rich FitzJohn

Last Published

June 13th, 2013

Functions in diversitree (0.9-5)

asr-bisse

Ancestral State Reconstruction Under BiSSE
diversitree-deprecated

Deprecated and Defunct Functions in Diversitree
find.mle

Maximimum Likelihood Inference
make.bisse

Binary State Speciation and Extinction Model
make.mkn

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

Multiple State Speciation and Extinction Model: Split Models
check

Check Capabilities of the Diversitree Install
history.from.sim

Extract Character Histories From Simulations
make.geosse.split

Geographic State Speciation and Extinction Model: Split Models
make.musse.multitrait

MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
mcmc

Simple Markov Chain Monte Carlo with Slice Sampling
make.geosse

Geographic State Speciation and Extinction Model
make.bd

Constant Rate Birth-Death Models
make.musse.td

Multiple State Speciation and Extinction Model: Time Dependent Models
protect

Protect Function Evaluations
make.musse

MuSSE: Multi-State Speciation and Extinction
make.bd.t

Time-varing Birth-Death Models
big.brother

Verbosely Track Function Evaluations
make.bd.split

Constant Rate Birth-Death Models: Split Models
make.quasse.split

Quantitative State Speciation and Extinction Model: Split Models
profiles.plot

Plot Marginal Distributions from MCMC
make.quasse

Quantitative State Speciation and Extinction Model
utilities

Utility Functions
make.bisseness

Binary State Speciation and Extinction (Node Enhanced State Shift) Model
make.bisse.td

Binary State Speciation and Extinction Model: Time Dependant Models
quasse-common

Support Functions for QuaSSE Models
simulate

Evolve Birth-Death Trees
make.prior

Simple Prior Functions
asr-mkn

Ancestral State Reconstruction Under Mk2/Mkn
constrain

Constrain Parameters of a Model
geosse.phy

Example GeoSSE Tree
make.bm

Brownian Motion and Ornstein-Uhlenbeck Character Evolution
trait.plot

Plot a Phylogeny and Traits
sim.character

Simulate a Character Distribution on a Tree
set.defaults

Set Default Arguments of a Function
argnames

Argument Names for Vector-Argument Functions
asr

Ancestral State Reconstruction
Constants

Constants Used by Diversitree
make.classe

Cladogenetic State change Speciation and Extinction Model
make.clade.tree

Make a "Clade Tree"
plot.history

Plot Character History
combine

Combine Several Likelihood Functions Multiplicatively
make.bisse.split

Binary State Speciation and Extinction Model: Split Models