R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(phylobase)
> library(ape)

Attaching package: 'ape'

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

    edges

> 
> ## set.seed(1)
> ## t0A <- rcoal(5)
> t0 <- read.tree(text="((t4:0.3210275554,(t2:0.2724586465,t3:0.2724586465):0.0485689089):0.1397952619,(t5:0.07551818331,t1:0.07551818331):0.385304634);")
> ## hack around variability in ape:
> ##   read.tree() and rcoal() produce sets of
> ##     elements in different orders
> t0 <- unclass(t0)[c("edge","edge.length","tip.label","Nnode")]
> class(t0) <- "phylo"
> 
> ## phylo -> phylo4 -> phylo
> t1 <- as(t0,"phylo4")
> t5 <- as(t1,"phylo")
Warning message:
In asMethod(object) : trees with unknown order may be unsafe in ape
> stopifnot(identical(t0,t5))
> 
> ## phylo4 -> phylo4vcov -> phylo4 -> phylo
> t2<-as(t1,"phylo4vcov")
Warning message:
In asMethod(object) : trees with unknown order may be unsafe in ape
> t3<-as(t2,"phylo4")
> t4<-as(t3,"phylo")
> stopifnot(identical(t4$edge,t0$edge) &&
+           identical(t4$tip.label,t0$tip.label) &&
+           identical(t4$Nnode,t0$Nnode) &&
+           max(abs(t4$edge.length-t0$edge.length))<1e-10)
> 
> ## UNROOTED
> t6 <- ape::unroot(t0)
> ## hack around ape conversion issues:
> ##  unroot() converts integer to double
> storage.mode(t6$edge) <- "integer"
> storage.mode(t6$Nnode) <- "integer"
> t7 <- as(as(t6,"phylo4"),"phylo")
> stopifnot(identical(t6,t7))
> 
> 
> ## EXPLICIT ROOT EDGE
> t8 <- t0
> t8$root.edge <- 0.5
> t9 <- as(as(t8,"phylo4"),"phylo")
Warning message:
In asMethod(object) : trees with unknown order may be unsafe in ape
> stopifnot(identical(t8,t9))
> 
> proc.time()
   user  system elapsed 
   2.00    0.28    2.25