pharmaverse / pharmaverse/rtables

add_overall_col does not inherit colcounts from previous split

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Description

I would like to display N=xx for a total column but this option is not available from the function:

adsl <- data.frame(
  ARM = c("Placebo", "Placebo", "Treatment A", "Treatment A", "Treatment B", "Treatment B"),
  AGE = c(25, 30, 22, 28, 19, 45),
  SEX = c("Male", "Female", "Male", "Female", "Female", "Female")
)

add_combo <- rtables::add_combo_facet(
  "Combined",
  label = "Combined",
  levels = c("Treatment A", "Treatment B")
)

rm_combo_from_placebo <- cond_rm_facets(
  facets = "Combined",
  ancestor_pos = NA,
  value = " ",
  split = "ARM"
)

mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))

basic_table() %>%
  split_cols_by("ARM", split_fun = mysplit, show_colcounts = TRUE, colcount_format = "N=xx") %>%
  add_overall_col("Total") %>%
  append_topleft("Mean Age \\super a") %>%
  analyze("AGE") %>%
  build_table(df = adsl)

                    Placebo   Treatment A   Treatment B   Combined        
Mean Age \super a     N=2         N=2           N=2         N=4      Total
——————————————————————————————————————————————————————————————————————————
Mean                 27.50       25.00         32.00       28.50     28.17

The only way of displaying the N = xx is to pass the arguments to basic_table, which is not always desired. Can add_overall_col be updated to fix this?

basic_table(show_colcounts = TRUE, colcount_format = "N=xx") %>%
  split_cols_by("ARM", split_fun = mysplit) %>%
  add_overall_col("Total") %>%
  append_topleft("Mean Age \\super a") %>%
  analyze("AGE") %>%
  build_table(df = adsl)

                    Placebo   Treatment A   Treatment B   Combined   Total
Mean Age \super a     N=2         N=2           N=2         N=4       N=6 
——————————————————————————————————————————————————————————————————————————
Mean                 27.50       25.00         32.00       28.50     28.17

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the add_overall_col and basic_table behavior shown in the reproduction, comparing the two example pipelines. Confirm that a Total column inherits show_colcounts and colcount_format from the preceding split, and verify that the rendered Total column displays N=6 without changing the existing subgroup counts.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
55/100

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