fix: R script and settings export missing volume unit simplification (#1190)

[Gero1999]

Issue

Closes #1190

Description

The volume unit simplification applied in tab_data.R (e.g. mg*L/mL → mg) was not being captured in the exported settings or R script. This happened because session$userData$units_table() only stored rows that the user explicitly edited in the Units modal — it used a default flag to track which rows were touched, and the automatic simplification never set that flag.

Root cause: The default column (added in #900 / PR #946) tracked edits by flagging rows as default = FALSE when the user clicked on them in the modal. Automatic changes (like the volume simplification) mutated the PKNCAdata object directly without going through the modal, so they were never flagged.

Fix: Replace the default flag with a value-based comparison: rows where PPSTRESU != PPORRESU are treated as changed. This captures both user edits and automatic simplifications, since any change to the display unit results in PPSTRESU differing from PPORRESU.

Changes

1. Save handler (units_table.R): Filter by PPSTRESU != PPORRESU instead of !default
2. Modal open (units_table.R): Stop adding default = TRUE/FALSE columns when building the table
3. Reactable (units_table.R): Remove hidden default column definition
4. Edit handler (units_table.R): Remove default <- FALSE assignment on edit
5. Global observer (units_table.R): Remove default from merge logic
6. Settings export (nca_setup.R, zip-utils.R): Remove filter(!default) %>% select(-default) — the units table already contains only changed rows
7. NCA run (tab_nca.R): Remove select(-any_of("default")) guard

Definition of Done

• Volume unit simplification is included in session$userData$units_table()
• Settings YAML export includes simplified volume units
• R script receives simplified volume units via custom_units_table
• User edits in the Units modal still work correctly
• default column fully removed from the units table flow
• Manual verification: R script produces same units as the Shiny app

How to test

1. Upload a dataset that has volume-based parameters (e.g. Vd, Vss)
2. Run NCA in the Shiny app — note the simplified units in the results
3. Export the settings YAML — verify it includes the simplified volume units
4. Export the R script — verify custom_units_table contains the simplified units
5. Run the R script — verify the output units match the Shiny app
6. Open the Units modal, change a unit manually, save — verify the change is captured in the settings export
7. Re-open the Units modal — verify the manual change persists

Contributor checklist

• Code passes lintr checks
• Code passes all unit tests
• New logic covered by unit tests
• New logic is documented
• App or package changes are reflected in NEWS
• Package version is incremented
• R script works with the new implementation (if applicable)
• Settings upload works with the new implementation (if applicable)
• If any .scss change was done, run data-raw/compile_css.R

Notes to reviewer

• The default column was introduced in PR Enhancement: settings file saves only edited units #946 (issue Enhancement: unit settings only manual changes and not entire units table #900). This PR removes it entirely in favor of value-based detection.
• Edge case: if a user sets PPSTRESU back to equal PPORRESU, that row is correctly treated as unchanged (no need to persist it).
• R is not available in the dev container, so devtools::document(), lintr, and tests could not be run locally."

[Copilot]

Pull request overview

Fixes an export mismatch in the Shiny NCA workflow where automatic unit simplifications (not performed via the Units modal) were not reflected in exported settings or generated R scripts.

Changes:

• Replace the previous edit-tracking default flag with value-based detection of unit changes (PPSTRESU != PPORRESU).
• Remove default column handling across Units modal plumbing and export paths.
• Add an observer to auto-populate session$userData$units_table() from pknca_data() when units differ from defaults.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
inst/shiny/modules/tab_nca/units_table.R	Removes default flag usage; switches to value-based “changed unit” filtering.
inst/shiny/modules/tab_nca/nca_setup.R	Removes export-time filtering/stripping of default from units settings.
inst/shiny/modules/tab_nca.R	Auto-populates units_table based on PPSTRESU != PPORRESU; removes default drop guard.
inst/shiny/functions/zip-utils.R	Stops filtering units by default during ZIP settings export.
NEWS.md	Documents the bug fix and the new change-detection behavior.
DESCRIPTION	Bumps package version.

Comments suppressed due to low confidence (3)

inst/shiny/modules/tab_nca/units_table.R:39

• dplyr::rows_update() can error if custom_units contains columns not present in default_units (e.g., older settings uploads or other sources adding extra cols). Elsewhere the codebase defensively subsets the update table to shared columns before calling rows_update() (see R/PKNCA.R where custom_units_table[, common_cols, drop = FALSE] is used). Consider applying the same pattern here by restricting custom_units to intersect(names(default_units), names(custom_units)) before the update.

      if (!is.null(session$userData$units_table())) {
        custom_units <- session$userData$units_table()
        by_cols <- intersect(names(default_units), names(custom_units))
        by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
        dplyr::rows_update(
          default_units,
          custom_units,
          by = by_cols,
          unmatched = "ignore"

inst/shiny/modules/tab_nca/units_table.R:212

• Same as above: rows_update() is passed custom_units without trimming to shared columns. To avoid runtime errors when session$userData$units_table() includes extra columns (e.g., from uploaded settings), subset custom_units to the shared column set before updating default_units (consistent with R/PKNCA.R).

      custom_units <- session$userData$units_table()
      by_cols <- intersect(names(default_units), names(custom_units))
      by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
      dplyr::rows_update(
        default_units,
        custom_units,
        by = by_cols,
        unmatched = "ignore"
      ) %>%

inst/shiny/modules/tab_nca.R:160

• When applying custom_units via rows_update(), consider subsetting custom_units to the shared column set (intersect(names(processed_pknca_data$units), names(custom_units))) before updating. This matches the defensive pattern in R/PKNCA.R and avoids potential errors if session$userData$units_table() ever carries extra columns (e.g., from settings upload).

          custom_units <- session$userData$units_table()
          by_cols <- intersect(names(processed_pknca_data$units), names(custom_units))
          by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
          processed_pknca_data$units <- rows_update(
            processed_pknca_data$units,
            custom_units,
            by = by_cols,
            unmatched = "ignore"

[Copilot]

The save handler now persists only rows where PPSTRESU != PPORRESU. This drops user changes where only conversion_factor was edited (allowed via editable = c("PPSTRESU", "conversion_factor")) while keeping the unit label unchanged, so those changes won’t be exported/applied. Consider treating a row as changed when either PPSTRESU != PPORRESU OR conversion_factor != 1 (with appropriate NA handling).

Suggested change

	dplyr::filter(!is.na(PPSTRESU), !is.na(PPORRESU), PPSTRESU != PPORRESU) %>%
	dplyr::filter(
	(!is.na(PPSTRESU) & !is.na(PPORRESU) & PPSTRESU != PPORRESU) |
	dplyr::coalesce(conversion_factor, 1) != 1
	) %>%