Geniefit: A function to fit coalescent models to a given phylogenetic...

In xiangfstats/GenieR: Inference of demographic history from phylogeny

Description

A function to fit coalescent models to a given phylogenetic tree.

Usage

Geniefit(phy, Model, start, upper, lower, Rcpp = F, MCMC = F, sig = 0.1,
  run = 10000)

Arguments

phy	A phylogenetic tree.
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).
start	Initial values for the parameters to be optimized over.
lower,	upper Bounds on the variables.
Rcpp	Calculation is based on C++ code when it is True and on R code when it is False.
MCMC	MCMC simulation is run when it is true, and not run when it is False. The default prior is uniform given the lower and upper.
sig	MCMC simulation step size.
run	Number of MCMC simulation.

Value

Parameters estimation of a given model, loglikelihood and AIC

Author(s)

Fei Xiang ([e-mail])

Examples

library(ape)
t1=rcoal(20)
Geniefit(t1,Model="expo",start=c(100,.1),upper=Inf,lower=0)
Geniefit(t1,Model="expo",start=c(100,.1),upper=Inf,lower=0,Rcpp=T)
###a MCMC simulation included##
f=Geniefit(t1,Model="expo",start=c(100,.1),upper=Inf,lower=0,MCMC=T,sig=.1,run=10000)
acf(f$MCMC.simulation)

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