GTSUMMARY Table with TBL_STRATA2: Zero count rows & Level ordering issue

This is a continuation of my question posted here. I am still facing some issues with usage of tbl_summary. For code below, I have forced TRT01A, PARAMCD etc. as factors. This helps me generate consistent shell data with zero counts and provides ability to control the display order in table body.

# Load data
advs <- pharmaverseadam::advs %>%
  filter(SAFFL == "Y" & !is.na(ANRIND)) %>%
  select(c(USUBJID, TRT01A, PARAMCD, PARAM, AVISIT, AVISITN, ADT, AVAL, ANRIND)) |> 
  mutate(TRT01AN = case_when(
    TRT01A == 'Xanomeline High Dose' ~ 1,
    TRT01A == 'Xanomeline Low Dose' ~ 2,
    TRT01A == 'Placebo' ~ 3
  ))

# Summary prior to process
advs.smr <- advs %>%
  group_by(USUBJID, TRT01A, TRT01AN, PARAMCD, PARAM) %>%
  # Can use slice_max or summarize
  summarise(AVL.NRIND = max(ANRIND, na.rm = TRUE), .groups = 'drop') |> 
  arrange(USUBJID, PARAMCD) |>
  mutate(
    TRT01A = factor(TRT01A, levels = unique(TRT01A[order(TRT01AN)])),
    PARAMCD = factor(PARAMCD, levels = c("SYSBP", "DIABP", "TEMP")),
    AVL.NRIND = factor(AVL.NRIND, levels = sort(unique(AVL.NRIND))[order(c(3,2,1))])
  ) |> 
  filter((PARAMCD == 'SYSBP' & !grepl("2$", USUBJID)) | (PARAMCD == 'DIABP' & !grepl("3$", USUBJID))|(PARAMCD == 'TEMP' & !grepl("1$", USUBJID)))

Using above source data tbl_summary with percent=adsl call have issues. From below code, tbl.smry1 can generate output successfully, whereas the tbl.smry2 fails.

tbl.smry1 <- advs.smr |> 
  tbl_strata2(
    strata = PARAMCD,
    ~ .x |> 
      tbl_summary(
        include = AVL.NRIND,
        by = TRT01A,
        label = list(AVL.NRIND = .y),
        percent = "column"
      ) |> 
      add_overall(last = TRUE),
    .combine_with = "tbl_stack",
    .combine_args = list(group_header = NULL)
  )

tbl.smry2 <- advs.smr |> 
  tbl_strata2(
    strata = PARAMCD,
    ~ .x |> 
      tbl_summary(
        include = AVL.NRIND,
        by = TRT01A,
        label = list(AVL.NRIND = .y),
        percent = adsl
      ) |> 
      add_overall(last = TRUE),
    .combine_with = "tbl_stack",
    .combine_args = list(group_header = NULL)
  )

Please let me know if I am missing something here. Output from tbl.smry1 below with zero count rows and PARAMCD, Treatment, ANRIND levels in order as forced using factor.

I think there were two issues here:

1. adsl was missing the pharmaverseadam::adsl prefix.
2. The treatment variable was character in adsl and a factor in advs. (I should have better messaging when there is a mis-match, however. I'll add that.)

library(tidyverse)
library(gtsummary)
packageVersion("gtsummary")
#> [1] '2.4.0.9002'

advs <- pharmaverseadam::advs %>%
  filter(SAFFL == "Y", !is.na(ANRIND), PARAMCD %in% c("SYSBP", "DIABP", "TEMP")) %>%
  select(c(USUBJID, TRT01A, PARAMCD, PARAM, AVISIT, AVISITN, ADT, AVAL, ANRIND)) |> 
  mutate(
    TRT01A = factor(TRT01A, levels = c('Xanomeline High Dose', 'Xanomeline Low Dose', 'Placebo'))
  )

# Summary prior to process
advs.smr <- advs %>%
  group_by(USUBJID, TRT01A, PARAMCD, PARAM) %>%
  # Can use slice_max or summarize
  summarise(AVL.NRIND = max(ANRIND, na.rm = TRUE), .groups = 'drop') |> 
  mutate(
    PARAMCD = factor(PARAMCD, levels = c("SYSBP", "DIABP", "TEMP")),
    AVL.NRIND = factor(AVL.NRIND, levels = sort(unique(AVL.NRIND))[order(c(3,2,1))])
  )

advs.smr |> 
  tbl_strata2(
    strata = PARAMCD,
    ~ .x |> 
      tbl_summary(
        include = AVL.NRIND,
        by = TRT01A,
        label = list(AVL.NRIND = .y),
        percent = 
          pharmaverseadam::adsl |> 
          mutate(
            TRT01A = factor(TRT01A, levels = c('Xanomeline High Dose', 'Xanomeline Low Dose', 'Placebo'))
          )
      ) |> 
      add_overall(last = TRUE),
    .combine_with = "tbl_stack",
    .combine_args = list(group_header = NULL)
  ) |> 
  bold_labels() |> 
  # convert to markdown to display on stackoverflow
  as_kable()

^{Created on 2025-10-07 with reprex v2.1.1}