read.nextstrain.json fails on divergence trees

[CecileTK]

Description of the issue

I've recently faced issues when using the function read.nextstrain.json on divergence trees (with divergence units in number of mutations). When using it on a json file (zika-divergence.json) obtained from a modified version of the Zika Nextstrain workflow,, I obtain the following error:

Session Info

library(treeio)
read.nextstrain.json("zika-divergence.json")

Error in `dplyr::bind_rows()`:
! Can't combine `..1$div` <integer> and `..2$div` <character>.
Run `rlang::last_trace()` to see where the error occurred.

Proposed solution

Playing with the source code, it looks like the error comes from the following line of code, with some nodes being loaded with a div variable as an integer and some as a character:

treeio/R/nextstrain.json.R

Line 53 in 9504617

dat <- dplyr::bind_rows(as.list(id[["data"]])) %>% dplyr::mutate_if(check_num, as.numeric)

Locally, I've managed to solve this by replacing:

treeio/R/nextstrain.json.R

Lines 39 to 43 in 9504617

	if ('div' %in% colnames(id[['data']][[id[['id']]]])){
	parent.index <- id[['data']][[id[['id']]]][['parentID']]
	id[['data']][[id[['id']]]][['branch.length']] <- as.numeric(id[['data']][[id[['id']]]][['div']]) -
	as.numeric(id[['data']][[parent.index]][['div']])
	}

by:

if ('div' %in% colnames(id[['data']][[id[['id']]]])){ 
     parent.index <- id[['data']][[id[['id']]]][['parentID']] 

     # Systematically converting div to a numeric value
     id[["data"]][[id[["id"]]]][["div"]] <- as.numeric(id[["data"]][[id[["id"]]]][["div"]])
     
     id[['data']][[id[['id']]]][['branch.length']] <- id[['data']][[id[['id']]]][['div']] -  
         as.numeric(id[['data']][[parent.index]][['div']]) 
 } 

I'd be happy to submit a pull request regarding this. Would you have a preference regarding how to do this and whether it might be valuable to also add the json file (zika-divergence.json) ? I also noticed that read.nextstrain.json does not have a testing file. Would it make sense to include all of this as part of a testing file? If so, do you have suggestions on what the testing should check?

Thank you!

[BaylorSci]

I would also like some follow up on this. I have recently tried to use the package to look at a nextstrain JSON file, with the same error message when loading:
read.nextstrain.json("./diseasex_genome_new_name.json")
This command returned the following error:
Error indplyr::bind_rows(): ! Can't combine ..1$num_date<double> and..3$num_date<character>. Runrlang::last_trace()` to see where the error occurred.

rlang::last_trace()
<error/vctrs_error_ptype2>
Error in dplyr::bind_rows():
! Can't combine ..1$num_date and ..3$num_date .

---

Backtrace:
▆

1. ├─global read.nextstrain.json("./diseasex_genome_new_name.json")
2. │ └─global parser_children(x$tree)
3. │ └─base::lapply(...)
4. │ └─global FUN(X[[i]], ...)
5. │ └─base::lapply(...)
6. │ └─global FUN(X[[i]], ...)
7. │ ├─dplyr::bind_rows(as.list(id[["data"]])) %>% ...
8. │ └─dplyr::bind_rows(as.list(id[["data"]]))
9. └─dplyr::mutate_if(., check_num, as.numeric)
10. └─dplyr:::check_grouped(.tbl, "mutate", "if")

11. └─dplyr::is_grouped_df(tbl)
    

Run rlang::last_trace(drop = FALSE) to see 10 hidden frames.
`
Note that even with the substitution outlined above, this did not correct the issue.

Are nextstrain JSON files still supported?

Session info:
`R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] ggtree_3.12.0 jsonlite_2.0.0 ape_5.8-1 treeio_1.28.0 lubridate_1.9.4 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] yulab.utils_0.2.1 utf8_1.2.6 rappdirs_0.3.3 generics_0.1.4 tidyr_1.3.1 ggplotify_0.1.2
[7] lattice_0.22-6 digest_0.6.37 magrittr_2.0.3 evaluate_1.0.5 grid_4.4.1 timechange_0.3.0
[13] RColorBrewer_1.1-3 fastmap_1.2.0 BiocManager_1.30.26 purrr_1.1.0 aplot_0.2.9 scales_1.4.0
[19] lazyeval_0.2.2 cli_3.6.4 rlang_1.1.5 crayon_1.5.3 tidytree_0.4.6 withr_3.0.2
[25] yaml_2.3.10 tools_4.4.1 parallel_4.4.1 ggplot2_4.0.0 vctrs_0.6.5 R6_2.6.1
[31] gridGraphics_0.5-1 lifecycle_1.0.4 fs_1.6.6 ggfun_0.2.0 pkgconfig_2.0.3 pillar_1.11.1
[37] gtable_0.3.6 glue_1.8.0 Rcpp_1.1.0 xfun_0.51 tibble_3.2.1 tidyselect_1.2.1
[43] rstudioapi_0.17.1 knitr_1.50 farver_2.1.2 htmltools_0.5.8.1 nlme_3.1-164 patchwork_1.3.2
[49] rmarkdown_2.29 compiler_4.4.1 S7_0.2.0 `