rootedTriple: Compare expected and sample frequencies of topological rooted triples.

Description

For a given species tree with population sizes, compares the expected frequencies of rooted triples to empirical frequencies in a sample of gene trees, using Chi-squared tests with 2 d.f. The exact and estimated internal branch length (in coalescent units) of the rooted triple in the species tree are also computed for comparison. A single test can be performed on the entire gene tree sample, or multiple tests on subsamples.

Usage

rootedTriple(
  stree,
  popSizes,
  gtSample,
  taxon1,
  taxon2,
  taxon3,
  subsampleSize = FALSE
)

Arguments

stree

An object of class phylo containing a rooted metric species tree. Edge lengths are in number of generations.

popSizes

An ordered list containing constant population sizes for each species tree edge, for a haploid organism. Sizes should be doubled for diploids. If stree has k edges, then popSizes must have k+1 elements, with the final entry for the population ancestral to the root.

gtSample

An object of class multiPhylo holding a sample of gene trees from a simulation. Taxon labels on gene trees must be identical to those on stree.

taxon1

A string specifying one taxon on stree.

taxon2

A string specifying a second taxon on stree, distinct from taxon1.

taxon3

A string specifying a third taxon on stree, distinct from taxon1, taxon2.

subsampleSize

A positive integer or FALSE, giving size of subsamples of gtSample to analyze.

Value

If subsampleSize is FALSE, returns an object of type rootedTripleOutput which contains a table $TripletCounts of empirical and expected rooted triple counts, a p-value $pv from the Chi-squared test, and a column $InternalEdge of estimated and exact internal edge lengths. If subsampleSize is TRUE, returns NULL but produces several plots.

Details

When subsampleSize is FALSE the Chi-squared test is performed using all gene trees in gtSample. Results are reported in tabular form in the console.

When subsampleSize is positive, the N trees in gtSample will be partitioned into N/subsampleSize subsamples, with a Chi-squared test performed for each. Histograms are plotted for (1) the p-values for the Chi-squared tests on subsamples, and (2) subsample estimates of the internal branch length for the rooted triple on the species tree, with the true value marked.

Three distinct taxon names must be supplied, all of which must occur on stree and in each of the gene trees in the sample.

Examples

Run this code

# NOT RUN {
stree=read.tree(text="((((a:10000,b:10000):10000,c:20000):10000,d:30000):10000,e:40000);")
pops=c(15000,25000,10000,1,1,1,1,1,12000)
gts=read.tree(file=system.file("extdata","genetreeSample",package="MSCsimtester"))
rootedTriple(stree,pops,gts,"a","b","c")
rootedTriple(stree,pops,gts,"a","b","c",1000) 
# }