as.treedata creating label.x and label.y columns in some cases

[nick-youngblut]

The expected result of using as.treedata, according to the example in the function docs:

library(ape)
library(dplyr)
set.seed(2017)
tree <- rtree(4)
d <- tibble(label = paste0('t', 1:4),
            trait = rnorm(4))
x <- as_tibble(tree)
full_join(x, d, by = 'label') %>% 
  as.treedata

Output:

'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 4 tips and 3 internal nodes.

Tip labels:
  t4, t1, t3, t2

Rooted; includes branch lengths.

with the following features available:
  'trait'.

# The associated data tibble abstraction: 7 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
   node label isTip  trait
  <int> <chr> <lgl>  <dbl>
1     1 t4    TRUE   0.943
2     2 t1    TRUE  -0.171
3     3 t3    TRUE   0.570
4     4 t2    TRUE  -0.283
5     5 NA    FALSE NA    
6     6 NA    FALSE NA    
7     7 NA    FALSE NA   

reprex of the issue

library(treeio, warn.conflicts = FALSE)
library(ggtree, warn.conflicts = FALSE)

df = data.frame(parent = c(5,7,7,6,5,5,6),
                node = c(1,2,3,4,5,6,7),
                label = c('t4','t1','t3','t2',NA,NA,NA))
as.treedata(df)

Output:

'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 4 tips and 3 internal nodes.

Tip labels:
  1, 4, 2, 3
Node labels:
  5, 6, 7

Rooted; no branch lengths.

with the following features available:
  'label'.

# The associated data tibble abstraction: 7 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
   node label.x isTip label.y
  <int> <chr>   <lgl> <chr>  
1     1 1       TRUE  t4     
2     2 4       TRUE  t2     
3     3 2       TRUE  t1     
4     4 3       TRUE  t3     
5     5 5       FALSE NA     
6     6 6       FALSE NA     
7     7 7       FALSE NA 

sessionInfo

R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] treeio_1.20.2   ggtree_3.4.4    RPostgres_1.4.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9         pillar_1.8.1       compiler_4.2.1     yulab.utils_0.0.5 
 [5] tools_4.2.1        digest_0.6.29      bit_4.0.4          aplot_0.1.7       
 [9] viridisLite_0.4.1  jsonlite_1.8.2     tidytree_0.4.1     lifecycle_1.0.2   
[13] tibble_3.1.8       nlme_3.1-157       gtable_0.3.1       lattice_0.20-45   
[17] pkgconfig_2.0.3    rlang_1.0.6        cli_3.4.1          DBI_1.1.3         
[21] ggplotify_0.1.0    patchwork_1.1.2    parallel_4.2.1     fastmap_1.1.0     
[25] httr_1.4.4         dplyr_1.0.10       htmlwidgets_1.5.4  hms_1.1.2         
[29] generics_0.1.3     vctrs_0.4.2        gridGraphics_0.5-1 DT_0.25           
[33] bit64_4.0.5        grid_4.2.1         tidyselect_1.1.2   data.table_1.14.2 
[37] glue_1.6.2         R6_2.5.1           plotly_4.10.0      fansi_1.0.3       
[41] blob_1.2.3         ggplot2_3.3.6      purrr_0.3.4        tidyr_1.2.1       
[45] magrittr_2.0.3     htmltools_0.5.3    ellipsis_0.3.2     scales_1.2.1      
[49] assertthat_0.2.1   ape_5.6-2          colorspace_2.0-3   renv_0.15.5       
[53] utf8_1.2.2         lazyeval_0.2.2     munsell_0.5.0      ggfun_0.0.7