addtips: Compare and add tips into new treestructure object

In emvolz-phylodynamics/treestructure: Detect Population Structure Within Phylogenetic Trees

Compare and add tips into new treestructure object

Description

Compares a new input tree to an old treestructure fit and merges tips into a new treestructure object. Tips in the new tree that are not in the new treestructure will be merged. Merging is carried out based on a phylogenetic criterion. The new tips are added to the cluster which shares its MRCA (most recent common ancestor).

Usage

addtips(trst, tre)

Arguments

trst	Original treestructure fit that that will be updated.
tre	A new tree (ape::phylo) which may contain samples not in trst. This tree must be rooted, but does not need to be time-scaled or binary.

Value

A new treestructure fit.

Author(s)

Erik Volz

Examples

set.seed(072023)
# simulate two trees and bind them to simulate structure
tr1 <- ape::rcoal( 50 )
tr2 <- ape::rcoal( 100 )
tr1$tip.label <- gsub(tr1$tip.label, patt = 't', rep = 's')
tr1$edge.length <- tr1$edge.length*.5
tr1$root.edge <- 1
tr2$root.edge <- 1
tr <- ape::bind.tree(tr1, tr2, position = .5 ) |> ape::multi2di()

# subsample the tree to simulating missing tips and estimate structure
ex <- sample( tr$tip.label, size = 30, replace = FALSE)
tr0 <- ape::drop.tip( tr, ex )
(s0 <- treestructure::trestruct( tr0 ))

# assign structure to the previously missing tips
(s <- treestructure::addtips( s0, tr ))

emvolz-phylodynamics/treestructure documentation built on June 11, 2025, 11:04 a.m.