GetPermutationWeightsAcrossSubsamples: Calculate tip label degeneracy weights for a set of trees

In phrapl: Phylogeography using Approximate Likelihood

Description

This function calculates weights for a tree or set of trees (typically subsampled trees) based on the degeneracy of tip lables (i.e., the proportion of times that permuting labels across a tree results in the same topology). These weights are applied during a grid or heuristic search in phrapl to obtain a more accurate estimate of the log likelihood of an observed tree given trees expected under a given model.

Usage

GetPermutationWeightsAcrossSubsamples(popAssignments,observedTrees)

Arguments

popAssignments	A list of vectors (typically only one vector will be specified) that define the number of tips per population included in the observed trees (usually these will be subsampled trees).
observedTrees	Multiphylo object containing the subsampled trees (outputted from PrepSubsampling)

Note

Because this function exhaustively permutes all possible tip lables across a tree, it can take a long time for large subsampled trees. For more information, please see the user manual.

Note

For more information, please see the user manual.

Author(s)

Nathan Jackson & Brian O'Meara

phrapl documentation built on May 2, 2019, 4:52 p.m.