get.transmat.phylo: Get transmat infection tree for each seed or for specified...

In thednainus/HIVepisimAnalysis: Functions to analyse results from network analysis

Get transmat infection tree for each seed or for specified seeds

Description

Separate a transmat object into different seedling event.

Usage

get.transmat.phylo(x, vertex.exit.times, by_areas = "all", max_value = NULL)

Arguments

x	An object of class "transmat", the output from get_transmat.
vertex.exit.times	optional numeric vector providing the time of departure of vertices, to be used to scale the lengths of branches reaching to the tips. Index position on vector corresponds to network id. NA indicates no departure, so branch will extend to the end of the tree.
by_areas	by_areas = "all" if interested in all seeds, or by_areas = "region" if interested in seeds for region only.
max_value	max value for comparison to select the seed values. It will select only seed values less than max_value for seeds from region only.

Details

Converts a transmat object containing information about the history of a simulated infection into a separated transmission matrix by seedling event.

This function was created using as base the function as.phylo.transmat

thednainus/HIVepisimAnalysis documentation built on Sept. 21, 2023, 7:32 a.m.