Learn R Programming
⚠️There's a newer version (0.10-1) of this package.Take me there.

diversitree (version 0.9-3)

diversitree: comparative phylogenetic analyses 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. 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.

Copy Link

Version

Install

install.packages('diversitree')

Monthly Downloads

901

Version

0.9-3

License

GPL (>= 2)

Maintainer

Richard FitzJohn

Last Published

May 8th, 2012

Functions in diversitree (0.9-3)

check

Check Capabilities of the Diversitree Install
make.mkn.deriv

Mk2 and Mk-n Models of character evolution [temporary extension with derivatives]
plot.history

Plot Character History
make.bd

Constant Rate Birth-Death Models
geosse.phy

Example GeoSSE Tree
make.geosse

Geographic State Speciation and Extinction Model
make.quasse.split

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

Plot a Phylogeny and Traits
sim.character

Simulate a Character Distribution on a Tree
make.bm

Brownian Motion and Ornstein-Uhlenbeck Character Evolution
asr-mkn

Ancestral State Reconstruction Under Mk2/Mkn
Constants

Constants Used by Diversitree
set.defaults

Set Default Arguments of a Function
asr

Ancestral State Reconstruction
make.bd.t

Time-varing Birth-Death Models
big.brother

Verbosely Track Function Evaluations
make.classe

Cladogenetic State change Speciation and Extinction Model
make.bd.split

Constant Rate Birth-Death Models: Split Models
history.from.sim

Extract Character Histories From Simulations
asr-bisse

Ancestral State Reconstruction Under BiSSE
make.geosse.split

Geographic State Speciation and Extinction Model: Split Models
make.bisse

Binary State Speciation and Extinction Model
make.clade.tree

Make a "Clade Tree"
make.bisseness

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

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

MuSSE: Multi-State Speciation and Extinction
mcmc

Simple Markov Chain Monte Carlo with Slice Sampling
make.mkn

Mk2 and Mk-n Models of character evolution
find.mle

Maximimum Likelihood Inference
make.bisse.split

Binary State Speciation and Extinction Model: Split Models
make.bisse.td

Binary State Speciation and Extinction Model: Time Dependant Models
time

Support Functions for Time-varying Models
simulate

Evolve Birth-Death Trees
make.quasse

Quantitative State Speciation and Extinction Model
argnames

Argument Names for Vector-Argument Functions
diversitree-deprecated

Deprecated and Defunct Functions in Diversitree
make.prior

Simple Prior Functions
quasse-common

Support Functions for QuaSSE Models
profiles.plot

Plot Marginal Distributions from MCMC
combine

Combine Several Likelihood Functions Multiplicatively
constrain

Constrain Parameters of a Model
make.musse.td

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

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

Protect Function Evaluations