WhenFirstHit: When was a tree topology first hit?

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

When was a tree topology first hit?

Description

Reports when each tree in a list was first found by tree search. This information is read from the firstHit attribute if present. If not, trees are taken to be listed in the order in which they were found, and named according to the search iteration in which they were first hit - the situation when trees found by MaximizeParsimony() are saved to file.

Usage

WhenFirstHit(trees)

Arguments

trees

A list of trees, or a multiPhylo object.

Value

trees, with a firstHit attribute listing the number of trees hit for the first time in each search iteration.

Author(s)

Martin R. Smith ([e-mail])

See Also

• MaximizeParsimony()

Other utility functions: ClusterStrings(), QuartetResolution()

Examples

library("TreeTools", quietly = TRUE)
trees <- list(
   seed_00 = as.phylo(1, 8),
   ratch1_01 = as.phylo(2, 8),
   ratch1_02 = as.phylo(3, 8),
   ratch4_44 = as.phylo(4, 8),
   final_99 = as.phylo(5, 8)
)
attr(WhenFirstHit(trees), "firstHit")

TreeSearch documentation built on Aug. 26, 2023, 9:06 a.m.