getTreeIntervalsSlow: Intervals of a phylogenetic tree

In laduplessis/beastio: Functions for pre- and post-processing of BEAST and BEAST2 files.

Description

Function to get the coalescent and sampling intervals of a binary tree (the function also works for serially-sampled trees). The function returns a table with each row representing one of the intervals in the tree. This can be used to get the vector of speciation/transmission and sampling times for a phylogenetic tree.

Usage

getTreeIntervalsSlow(tree, decreasing = FALSE, raw = FALSE)

Arguments

tree	An object of class "phylo" from ape
decreasing	If FALSE intervals are ordered from the present into the past. If TRUE intervals are ordered from the tMRCA to the present.
raw	If TRUE return the raw table before reordering and calculating interval lengths or numbers of lineages. Mostly for debugging purposes.

Details

This is a deprecated version that is very slow on big trees (>10K nodes). This version is kept because it is easier to read and debug. Not using random access to arrays speeds up the initial setup.

See Also

getTreeIntervals

laduplessis/beastio documentation built on Dec. 14, 2021, 7:04 p.m.