In georgeshirreff/multiNe: Multiple Ne estimators

Methods to estimate effective population size

library(ape)
library(multiNe)
library(INLA)
library(adegenet)

There is a function for simulating trees under various functions of population size and other factors.

growing_trees<-simulate.tree(n=500,N=20,sampling="hetero")$out
plot(growing_trees[[1]])
conf.int<-Phylos2Skylines_anchor(trees=growing_trees,output_type="conf.int.plot",epsilon=0)

This can also be used to graph piecewise linear functions such as the output of INLA.

tree<-rmtree(N=2,n=50)[[1]]
result<-calculate.moller(tree,lengthout=100,L=1)
conf.int.skyline(result,epsilon=0.01,plot_type="linear")

library(phyclust)
sim_ms<-ms(nsam=5,nreps=10,"-T")
sim_genind<-ms2ms(sim_ms)

data(nancycats)
HENe(nancycats)

georgeshirreff/multiNe documentation built on May 17, 2019, 1:15 a.m.