mstackhouse
commented
10 months ago Here's a reduced example of the bug down to a reprex. The issue is with set_order_count_method() specifically for bycount with inner variable values that duplicate between outer variable values within a nested count layer. This is related to #75 as well.
test_adae <- data.frame(
SUBJID = c("1", "2", "3"),
AEBODSYS = c("Nervous system disorders", "Vascular system disorders", "Vascular system disorders"),
AEDECOD = c("Dizziness", "Dizziness", "other decod"),
TRT101A = c("TRT1", "TRT2", "TRT1")
)
test_adsl <- data.frame(
SUBJID = c("1", "2", "3"),
TRT101A = c("TRT1", "TRT2", "TRT1")
)
t1 <- Tplyr::tplyr_table(test_adae, TRT101A) |>
Tplyr::add_layer(
Tplyr::group_count(vars(AEBODSYS, AEDECOD)) |>
Tplyr::set_order_count_method("bycount")
)
table <- Tplyr::build(t1)
#> Error in `purrr::map()` at Tplyr/R/build.R:77:4:
#> ℹ In index: 1.
#> Caused by error in `[<-` at Tplyr/R/sort.R:745:6:
#> ! Assigned data `get_data_order_bycount(...)` must be compatible with
#> row subscript `-1`.
#> ✖ 1 row must be assigned.
#> ✖ Assigned data has 2 rows.
#> ℹ Row updates require a list value. Do you need `list()` or `as.list()`?
#> Caused by error in `vectbl_recycle_rhs_rows()`:
#> ! Can't recycle input of size 2 to size 1.
#> Backtrace:
#> ▆
#> 1. ├─Tplyr::build(t1)
#> 2. ├─Tplyr:::build.tplyr_table(t1) at Tplyr/R/build.R:51:4
#> 3. │ ├─base::tryCatch(...) at Tplyr/R/build.R:61:2
#> 4. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> 5. │ └─purrr::map(x$layers, process_formatting) at Tplyr/R/build.R:77:4
#> 6. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 7. │ ├─purrr:::with_indexed_errors(...)
#> 8. │ │ └─base::withCallingHandlers(...)
#> 9. │ ├─purrr:::call_with_cleanup(...)
#> 10. │ ├─Tplyr (local) .f(.x[[i]], ...)
#> 11. │ └─Tplyr:::process_formatting.count_layer(.x[[i]], ...) at Tplyr/R/build.R:145:2
#> 12. │ ├─Tplyr:::add_order_columns(x) at Tplyr/R/count.R:424:2
#> 13. │ └─Tplyr:::add_order_columns.count_layer(x) at Tplyr/R/sort.R:144:2
#> 14. │ └─base::evalq(...) at Tplyr/R/sort.R:162:2
#> 15. │ └─base::evalq(...)
#> 16. │ └─... %>% ungroup() at Tplyr/R/sort.R:209:6
#> 17. ├─dplyr::ungroup(.)
#> 18. ├─dplyr::do(...)
#> 19. ├─dplyr:::do.grouped_df(...)
#> 20. │ └─rlang::eval_tidy(args[[j]], mask)
#> 21. ├─Tplyr:::add_data_order_nested(...)
#> 22. │ ├─base::`[<-`(...) at Tplyr/R/sort.R:745:6
#> 23. │ └─tibble:::`[<-.tbl_df`(...) at Tplyr/R/sort.R:745:6
#> 24. │ └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
#> 25. │ └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
#> 26. │ ├─base::withCallingHandlers(...)
#> 27. │ └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
#> 28. │ └─vctrs::vec_assign(x, i, value)
#> 29. ├─vctrs:::stop_recycle_incompatible_size(...)
#> 30. │ └─vctrs:::stop_vctrs(...)
#> 31. │ └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
#> 32. │ └─rlang:::signal_abort(cnd, .file)
#> 33. │ └─base::signalCondition(cnd)
#> 34. ├─tibble (local) `<fn>`(`<vctrs___>`)
#> 35. │ └─tibble:::vectbl_recycle_rhs_rows(value, length(i), i_arg, value_arg, call)
#> 36. │ ├─base::withCallingHandlers(...)
#> 37. │ └─vctrs::vec_recycle(value[[j]], nrow)
#> 38. └─vctrs:::stop_recycle_incompatible_size(...)
#> 39. └─vctrs:::stop_vctrs(...)
#> 40. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)Created on 2023-11-03 with reprex v2.0.2
asbates
TYoungTradeCraft
Prerequisites
Build of Tplyr AE table where an AEDECOD is assigned multiple values of AEBODSYS
Description
Tplyr build produces an error when attempting to build an AE table where a single AEDECOD is assigned to multiple AEBODSYS values, which is permitted in MedDRA
Steps to Reproduce
Versions
Tplyr_1.1.0