negllc_log: Function to calculate the logistic of a logistic coalescent...

In xiangfstats/GenieR: Inference of demographic history from phylogeny

Description

Function to calculate the logistic of a logistic coalescent model

Usage

negllc_log(parr, t, A)

Arguments

parr	A parameter vector for population size, growth rate and logistic shape parameter.
t	A sampling and coalescent time vector.
A	A lineages vector

Value

loglikelihood of a logistic coalescent model.

Author(s)

Fei Xiang ([e-mail])

Examples

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

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