Simplify the logic in slope plots, add order option & allow download in ZIP

[Gero1999]

Description

This changes simplify the logic that makes the slope plots in order to make easier future implementations and also make able the download of all plots in a zip file easily. The advantages would be:

Features

• Slope order input. Users can group their plots in whatever way they want them to appear.

Enhancements

• All plots are generated, instead of only the rendered ones.
• The new function that generates plots is faster and more aligned with PKNCA (get_halflife_plot)
• Only modified plots are affected by changes, reducing unnecessary plot redraws
• Upstream, the PKNCA object is updated with the slope rules directly in setup.R, instead of in the post-processing of results. We no longer need to use filter_slopes
• We no longer use the custom is.included.hl or is.excluded.hl that then are used to build exclude_half.life. Instead we directly use the exclude_half.life & include_half.life columns
• Added more documentation and comments
• The new reactivity flow to create the plots that allows a simpler use of settings. We just simply need to udpate the dataset and/or manual slopes and everything will be auto-managed:

#' processed_pknca_data (input, from parent)
#'   └─> slope_selector_server
#'        ├──> plot_outputs (reactive, updated by processed_pknca_data changes)
#'        └──> ├> handle_plotly_click (updates manual_slopes on plot click)
#'                   └> handle_table_edits (updates manual_slopes on user edits & setting overrides)
#'                          └─> manual_slopes (output, used by parent to update processed_pknca_data)

Bugs fixed

• Pagination controls are less likely to break (unless you are a clicking psycho 💀)
• Exclusion/Inclusion of points or table edits won't reset subject search
• Units appear for the Y axis

Tests

• Setup FIXTURE_PKNCA_DATA obj will now contain the columns include_half.life, exclude_half.life

Definition of Done

Closes or contributes to #333 (I think with this the client interest is already satisfied)

• Grouping option for slopes plots
• Faceting so groups are all on one page

Closes #553

• Logic was simplified and code refactored
• All Slope Selector features work well without issues
• Make a folder Slope selector including its plots

How to test

How to test features not covered by unit tests.

Contributor checklist

• Code passes lintr checks
• Code passes all unit tests
• New logic covered by unit tests
• New logic is documented
• Package version is incremented

Notes to reviewer

Compare thoughtfully the feats of the plots to make sure I did not miss anything relevant.
Don't hesitate also to leave suggestions for refactoring or code comments that makes the code easier to read.

[Copilot]

Pull request overview

Copilot reviewed 37 out of 38 changed files in this pull request and generated 7 comments.

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[Copilot]

The inner_join on line 86 may fail or produce unexpected results if first_group contains NA values or if there's no matching row in the concentration data. Consider adding error handling or validation to ensure the join succeeds and that at least 2 rows exist before accessing the second element with [2].

Suggested change

	new_row <- cbind(
	first_group,
	data.frame(
	TYPE = "Exclusion",
	RANGE = paste0(
	inner_join(first_group, pknca_data()$conc$data)[[time_col]][2]
	),
	# Safely join to concentration data and derive a time value for the RANGE column
	joined_conc <- inner_join(first_group, pknca_data()$conc$data)
	if (!is.null(time_col) && time_col %in% names(joined_conc) && nrow(joined_conc) > 0) {
	if (nrow(joined_conc) >= 2) {
	range_value <- joined_conc[[time_col]][2]
	} else {
	# Fallback to the first available time if only one row is present
	range_value <- joined_conc[[time_col]][1]
	}
	} else {
	# If join fails or time column is unavailable, use NA to avoid runtime errors
	range_value <- NA_character_
	}
	new_row <- cbind(
	first_group,
	data.frame(
	TYPE = "Exclusion",
	RANGE = paste0(range_value),

[Copilot]

The search pattern on line 54 hardcodes "USUBJID" as the grouping variable for filtering plots. If the data uses a different subject identifier column name, this search will not work correctly. Consider making the subject column name configurable or dynamically detecting it from the pknca_data object.

[Gero1999]

@js3110 regarding the very specific user bugs:

If I add an exclusion, run NCA, then go back to setup and remove the exclusion, I get this error:
Warning: Error in if: missing value where TRUE/FALSE needed

This is fixed

If I run through the workflow quite fast, and add an exclusion, I clikc the run NCA buton then nothing happens. I wait a few seconds and click again then nothing happens, repeat. Then eventually it runs and it Runs NCA like 3 times. Has happened to me twice now so I know its a real bug- but hard to recreate unorganically...

This I was not able to replicate it neither here nor in main. Maybe was fixed with after the merge. Otherwise please share me a screen recording and the console messages and I will try to look into it

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@m-kolomanski regarding the suggestions:

Most of them were addressed. Some style changes specifically for get_halflife_plots.R I will in principle not implement them because they conflict with PKNCA style, and the function might likely be transferred there at some point

[js3110]

Hey @Gero1999 , thanks, the bugs from before don't seem to be there anymore!

Unfortunately I ran into some other issues:

If I add a selection it doesn't update the plot:

If I click all the way to the end, I then can't change page anymore:

I also got an error after adding the following selections/exclusions:

ERROR [2026-01-07 11:08:17] Error calculating NCA results:
ℹ In index: 13.
Caused by error in `assert_numeric_between()`:
! Please report a bug.
: Error with interval start=0, end=24.018: Assertion on 'lambda.z' failed: Element 1 is not > 0

It worked after I removed the selection. I tried a different selection and this time it worked (the plot updated but only after I ran the NCA)

I removed an exclusion and ran the NCA again, then when I went to add it back it added two rows to the table:

Now every time I try to add a new exclusion/selection it adds all the previous ones too:

Screen.Recording.2026-01-07.111559.mp4