Persist parameter exclusions in settings YAML

[Shaakon35]

Feature request

Manual parameter exclusions (from the Parameter Exclusions tab, PR #1040) are lost on page refresh or settings re-upload. They should be saved and restored via the settings YAML file.

What the settings file currently covers

The following are saved in the settings YAML and restored on upload:

Setting	Persisted	Restored on upload
Method (linear/log)	✅	✅
Analyte selection	✅	✅
Profile (ATPTREF) selection	✅	✅
PCSPEC selection	✅	✅
Min. points for half-life	✅	✅
Bioavailability route	✅	✅
Interval parameters	✅	✅
Flag rules (thresholds)	✅	✅
Unit overrides	✅	✅
Ratio table	✅	✅
Column mapping	✅	✅
Slope rules	✅	✅
Data filters	✅	✅
Time duplicate keys	✅	✅
NCA ran flag	✅	✅
Active tab	✅	✅
Data imputation settings	✅	✅
Slope manual selections	✅	✅

What is NOT covered (needs implementation)

Setting	Status
Parameter exclusions (manual row exclusions from Parameter Exclusions tab)	❌ Not persisted
Exploration plot configurations (saved plots, color/facet selections)	❌ Not persisted
General exclusions (row-level exclusions from General Exclusions tab)	❌ Not persisted

Proposed approach for parameter exclusions

1. Save: Add parameter_exclusions to the settings payload in nca_setup.R. Store as a list of {reason, rows} entries (the same structure as exclusion_list() in parameter_exclusions_server).

2. Restore: In parameter_exclusions_server, accept a settings_override reactive. When settings are loaded, populate exclusion_list() from the saved data.

3. Compatibility: Old settings files without parameter_exclusions should load without error (guard with !is.null()).

Related

• PR feat: parameter exclusion from TLG summaries via PPSUMFL/PPSUMRSN in ADPP (#1019) #1040 — Parameter exclusions feature
• Issue Add PK parameter exclusion from TLGs (ANL01FL in ADPP) #1019 — Original feature request