Compare and add tips into new treestructure object

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

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 ))
#> Finding splits under nodes: 121 
#> Finding splits under nodes: 121 163 
#> Finding splits under nodes: 121 142 
#> Call: 

#> treestructure::trestruct(tre = tr0)
#> 

#> Target FDR: 0.2 (bonferroni correction)
#> Global structure test: max|z| = 3.34 over 24 candidates, p = 0.02
#> Number of clusters: 3 
#> Number of partitions: 2 
#> NOTE: heterochronous sampling detected (overlap index 0.86). Under the coalescent null this
#>       can modestly inflate the realized FDR (up to ~2x at target 5% in our real-data study);
#>       see vignette("treestructure"). Deep clades whose most recent sample is old are most affected.
#> Number of taxa in each cluster:
#> 
#>  1  2  3 
#> 78 28 14 
#> Number of taxa in each partition:
#> 
#>  1  2 
#> 78 42 
#> ...

#> For complete data, use `as.data.frame(...)` 

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

#> treestructure::trestruct(tre = tr0)
#> 

#> Target FDR: 0.2 (bonferroni correction)
#> Global structure test: max|z| = 3.34 over 24 candidates, p = 0.02
#> Number of clusters: 3 
#> Number of partitions: 2 
#> NOTE: heterochronous sampling detected (overlap index 0.86). Under the coalescent null this
#>       can modestly inflate the realized FDR (up to ~2x at target 5% in our real-data study);
#>       see vignette("treestructure"). Deep clades whose most recent sample is old are most affected.
#> Number of taxa in each cluster:
#> 
#>   1   2   3 
#> 100  36  14 
#> Number of taxa in each partition:
#> 
#>   1   2 
#> 100  50 
#> ...

#> For complete data, use `as.data.frame(...)`