loglik: A function to calculate the log likelihood of a phylogenetic...

In xiangfstats/GenieR: Inference of demographic history from phylogeny

Description

A function to calculate the log likelihood of a phylogenetic tree given various coalescent models.

Usage

loglik(phy, parr, Model, Rcpp = F)

Arguments

phy	A phylogenetic tree.
parr	Parameters.
Model	A Model choice from const (constant population size), expo (exponetial growth),expan (expansion growth), log (logistic growth), step (piecewise constant), pexpan (piecewise expansion growth) and plog (piecewise logistic growth).
Rcpp	Calculation is based on C++ code when it is True and on R code when it is False.

Value

log likelihood of a phylogeny given a coalescent model and parameters.

Author(s)

Fei Xiang ([e-mail])

Examples

data(village)
system.time(loglik(village,c(100,1),Model="expo",Rcpp=T))
system.time(loglik(village,c(100,1),Model="expo",Rcpp=F))

xiangfstats/GenieR documentation built on May 4, 2019, 1:06 p.m.