addtips: Compares a new input tree to an old treestructure fit and...

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

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.

Description

Merging is carried out based on a phylogenetic criterion. The new tips are added to the cluster which shares its MRCA.

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 <[e-mail]>

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 March 1, 2025, 3:47 p.m.