R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
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> library(phylobase)
> library(ape)

Attaching package: 'ape'

The following object is masked from 'package:phylobase':

    edges

> data(geospiza)
> 
> gtree <- extractTree(geospiza)
> stopifnot(identical(gtree,prune(gtree,character(0))))
> 
> stopifnot(identical(tdata(subset(geospiza)),
+                     tdata(subset(geospiza, tipLabels(geospiza)))))
> 
> 
> tr <- read.tree(text="(((spA:0.2,(spB:0.1,spC:0.1):0.15):0.5,spD:0.7):0.2,spE:1):0.4;")
> phyd <- as(tr, "phylo4d")
> tipData(phyd) <- 1:5
> stopifnot(identical(phyd@data,subset(phyd,tipLabels(phyd))@data))
> 
> 
> proc.time()
   user  system elapsed 
   2.03    0.35    2.34