marginalTransitions: Expected transitions per site

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

Description

Compute the expected number of transitions aggregated across either nodes or edges

Arguments

model	rateModel object
aggregate	How expected numbers of transitions should be aggregated (within edge or node)
excludeNodes	Indicates nodes that should be excluded from the per-edge aggregated statistic (1-based). Only usable with aggregate = "edge".
excludeEdges	Indicates edges that should be excluded from the per-node aggregated statistic Only usable with aggregate = "node". (edge ids based on integer id of child, use plotTree(model) to view).
threads	number of threads to use

Value

a list of per node/edge matricies containing the expected number of allelic transitions. The rows are the ancestral allele and the columns are the descendant allele. The list ids are a character string that are either a site or edge (child) id depending on how you aggregated

ndukler/phyloGLM documentation built on Sept. 25, 2019, 9:17 p.m.