diversitree: comparative phylogenetic analyses of diversification

系統比較解析

> library(diversitree)

Loading required package: deSolve

Attaching package: 'deSolve'

The following object is masked from 'package:graphics':

    matplot

Loading required package: ape
Loading required package: subplex
Loading required package: Rcpp

バージョン: 0.9.7

関数名 概略
argnames Argument Names for Vector-Argument Functions
asr Ancestral State Reconstruction
asr.bisse Ancestral State Reconstruction Under BiSSE
asr.mkn Ancestral State Reconstruction Under Mk2/Mkn
check.fftC Check Capabilities of the Diversitree Install
combine Combine Several Likelihood Functions Multiplicatively
constant.x Support Functions for QuaSSE Models
constrain Constrain Parameters of a Model
find.mle Maximimum Likelihood Inference
geosse.phy Example GeoSSE Tree
get.descendants Utility Functions
history.from.sim.discrete Extract Character Histories From Simulations
make.bd Constant Rate Birth-Death Models
make.bd.split Constant Rate Birth-Death Models: Split Models
make.bd.t Time-varing Birth-Death Models
make.bisse Binary State Speciation and Extinction Model
make.bisse.split Binary State Speciation and Extinction Model: Split Models
make.bisse.td Binary State Speciation and Extinction Model: Time Dependant Models
make.bisseness Binary State Speciation and Extinction (Node Enhanced State Shift) Model
make.bm Brownian Motion and Related Models of Character Evolution
make.clade.tree Make a "Clade Tree"
make.classe Cladogenetic State change Speciation and Extinction Model
make.geosse Geographic State Speciation and Extinction Model
make.geosse.split Geographic State Speciation and Extinction Model: Split Models
make.geosse.t Geographic State Speciation and Extinction Model: Time Dependent Models
make.mkn Mk2 and Mk-n Models of character evolution
make.musse MuSSE: Multi-State Speciation and Extinction
make.musse.multitrait MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.musse.split Multiple State Speciation and Extinction Model: Split Models
make.musse.td Multiple State Speciation and Extinction Model: Time Dependent Models
make.pgls Phylogenetic Generalised Least Squares
make.prior Simple Prior Functions
make.quasse Quantitative State Speciation and Extinction Model
make.quasse.split Quantitative State Speciation and Extinction Model: Split Models
mcmc Simple Markov Chain Monte Carlo with Slice Sampling
plot.history Plot Character History
profiles.plot Plot Marginal Distributions from MCMC
set.defaults Set Default Arguments of a Function
sim.character Simulate a Character Distribution on a Tree
trait.plot Plot a Phylogeny and Traits
trees Evolve Birth-Death Trees

make.pgls

系統的一般化最小二乗法

simulate