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

> 
> set.seed(1)
> r1 <- rcoal(5)
> 
> ## trace("phylo4d", browser, signature = "phylo")
> ## untrace("phylo4d", signature = "phylo")
> tipdat <- data.frame(a=1:5,row.names=r1$tip.label)
> p1 <- phylo4d(r1,tip.data=tipdat,node.data=data.frame(a=6:9), match.data=FALSE)
> p2 <- prune(p1,1)
> summary(p2)

 Phylogenetic tree : as(x, "phylo4") 

 Number of tips    : 4 
 Number of nodes   : 3 
 Branch lengths:
        mean         : 0.252522 
        variance     : 0.02063627 
        distribution :
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.04857 0.17296 0.27246 0.25252 0.30889 0.46082 

Comparative data:

Tips: data.frame with 4 taxa and 1 variable(s) 

       a       
 Min.   :2.00  
 1st Qu.:2.75  
 Median :3.50  
 Mean   :3.50  
 3rd Qu.:4.25  
 Max.   :5.00  

Nodes: data.frame with 3 internal nodes and 1 variables 

       a      
 Min.   :6.0  
 1st Qu.:6.5  
 Median :7.0  
 Mean   :7.0  
 3rd Qu.:7.5  
 Max.   :8.0  
> 
> ## from picante
> `phylo2phylog` <-
+ function(phy, ...) {
+     newick2phylog(write.tree(phy, multi.line = FALSE),...)
+ }
> 
> plot.phylo(as(p2,"phylo"))
Warning message:
In asMethod(object) : losing data while coercing phylo4d to phylo
> 
> proc.time()
   user  system elapsed 
   1.32    0.32    1.64