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

> tree.phylo <- read.tree(text="(((A,B)C,D),E);")  #only one node is labelled
> tree <- as(tree.phylo, "phylo4")
> 
> tree.phylo2 <- read.tree(text="(((A,B)C,D)F,E)G;")  # all nodes labelled
> tree2 <- as(tree.phylo2, "phylo4")
> 
> tip.data <- data.frame(size=c(1, 2, 3, 4))
> rownames(tip.data) <- c("A", "B", "E", "D")
> 
> treed <- phylo4d(tree, tip.data)
> dat2 <- data.frame(size=c(0,1,2), row.names=c("G", "F", "C"))
> 
> try(phylo4d(tree, node.data=dat2), silent = TRUE)  # error, cannot match data because no node labels on tree
> phylo4d(tree2, node.data=dat2) -> treed2  # OK tree labelled; has node data, no tip data 
> 
> plot(treed2) # works with a warning about no tip data to plot
Warning message:
In treePlot(x, ...) : tree has no tip data to plot
> tipData(treed2, empty.columns=FALSE) #returns empty 4-row data.frame
data frame with 0 columns and 4 rows
> 
> phylo4d(tree2, tip.data=tip.data, node.data=dat2) -> treed3 #node+tip data
> 
> plot(treed3)  # works
> tipData(treed3)  #works, but returns tips only
  size
A    1
B    2
D    4
E    3
> tdata(treed3, "all")
  size
A    1
B    2
D    4
E    3
G    0
F    1
C    2
> 
> print(tree)
  label node ancestor edge.length node.type
1     A    1        7          NA       tip
2     B    2        7          NA       tip
3     D    3        6          NA       tip
4     E    4        5          NA       tip
5  <NA>    5        0          NA      root
6  <NA>    6        5          NA  internal
7     C    7        6          NA  internal
> print(treed)
  label node ancestor edge.length node.type size
1     A    1        7          NA       tip    1
2     B    2        7          NA       tip    2
3     D    3        6          NA       tip    4
4     E    4        5          NA       tip    3
5  <NA>    5        0          NA      root   NA
6  <NA>    6        5          NA  internal   NA
7     C    7        6          NA  internal   NA
> 
> 
> proc.time()
   user  system elapsed 
   2.17    0.34    2.50