Resolve open TODOs and add missing documentation and tests

[h5hoang]

Issue

Closes #1299

Description

Resolves open TODOs, adds missing documentation and tests, fixes typos, and standardizes metadata CSV values across the codebase.

Task 1: Add documentation to units_table.R

• Replaced TODO with proper roxygen documentation for units_table_ui().

Task 2: Resolve TODO in flexible_violinboxplot.R

• Removed cut-off TODO comment; improved @param descriptions for xvars, colorvars, and varvalstofilter.

Task 3: Add tests for R/utils-plots.R

• Created tests/testthat/test-utils-plots.R with 9 tests covering .handle_tooltips() and error_plot().

Task 4: Standardize T/F to TRUE/FALSE in metadata CSV

• Updated can_* columns in data-raw/metadata_nca_parameters.csv and regenerated .rda.
• Fixed related bug in parameter_selection.R:462 where identical(can_exc, "T") was comparing a logical to a string (always FALSE). Changed to isTRUE(can_exc). Refer to the issue comment.

Task 5: Fix typo "miliseconds" → "milliseconds"

• Fixed in inst/shiny/www/index.js.

Task 6: Fix typo "infering" → "inferring"

• Fixed in 4 TLG option modules (8 occurrences). Also fixed resulting line-length lint violations.

Definition of Done

• units_table.R has proper roxygen documentation for UI function
• TODO in flexible_violinboxplot.R resolved — parameters documented, comment removed
• test-utils-plots.R created with tests for .handle_tooltips() and error_plot()
• metadata_nca_parameters.csv uses TRUE/FALSE in can_* columns, .rda regenerated
• Typo "miliseconds" fixed in index.js
• Typo "infering" fixed in TLG option modules

How to test

• Tests: Review logic makes sense
• Documentaiton: Review the doocumentation changes were applied
• The App keeps working regarding metadata_nca_parameters.csv (input widgets in NCA > Parameter Selection

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
• If a package dependency was added/changed, run data-raw/test_suggests_hidden.R

Notes to reviewer

Anything that the reviewer should know before tacking the pull request?

• Task 4 included a related bug fix: parameter_selection.R:462 used identical(can_exc, "T") which always returned FALSE because read.csv() converts unquoted T to logical TRUE. Changed to isTRUE(can_exc). See issue comment for details.

[Gero1999]

Nice work on this PR! Just to be very nitpicky:

Merge conflict risk: The T/F → TRUE/FALSE CSV rewrite touches every row, which will conflict with PRs #1245 that also modify this file to fix a bug found. Might be worthy be a bit careful while merging and making sure what was fixed there still remains here

Issue: This is my bad. The identical(can_exc, "T") was indeed always FALSE (logical vs string comparison), but the resulting behavior was actually correct. The can_excretion column indicates whether a parameter can be computed from excretion data — it's used for parameter matrix defaults, not for UI location. Only TYPE == "Urine" parameters (RCAMINT, FREXINT) are actually configurable in the Excretion tab.

Changing to isTRUE(can_exc) makes the condition work as written, but what was written was wrong — it now shows "Additional Analysis > Excretion" for ~30 standard parameters (CMAX, TMAX, etc.) that aren't available there. See the images below. To fix perhaps just remove the can_exc variable and simplify the condition to just if (type == "Urine").

Let me know if there are questions. Once you are done feel free to bump the package version. Overall good job! :)

[h5hoang]

Hi Gerardo! Thanks for the feedback!

I've addressed the concerns you had, it should run properly now. Attached are the screenshots that show that the "Additional Analysis > Excretion" is now limited to just these 5 params.

I also merged main and preserved the show_in_matrix_selection column from #1245 before re-applying the T/F → TRUE/FALSE fix.

[Gero1999]

Good job, LGTM!

Only thing would be to update the PR description for the later change made. But the solution itself is wonderful 😉

[AngelaManginelli]

I checked whether the "definition of done" was correctly implemented and did not fine any inconsistency. Thanks!