negllc_pexpan: Function to calculate the loglikelihood of a piecewise...

In xiangfstats/GenieR: Inference of demographic history from phylogeny

Description

Function to calculate the loglikelihood of a piecewise expansion coalescent model

Usage

negllc_pexpan(parr, t, A)

Arguments

parr	A parameter vector for population size, exponential growth rate and propotion to population size prior to change.
t	A sampling and coalescent time vector.
A	A lineages vector

Value

loglikelihood of a piecewise expansion coalescent model.

Author(s)

Fei Xiang ([e-mail])

Examples

library(ape)
t1=rcoal(20)
x=att(t1)
negllc_pexpan(c(1,1,.1), x$t, x$A)
library(minqa)
bobyqa(c(1,2,1),negllc_pexpan,lower=0,upper=Inf,t=x$t,A=x$A)
Geniefit(t1,Model="pexpan",start=c(10,2,1),upper=Inf,lower=0)
library(dfoptim)
nmkb(c(1,2,10),negllc_pexpan,lower=0,upper=Inf,t=x$t,A=x$A)

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