Bug fix: prevent PKNCA_impute_method_FALSE error from YAML impute_c0 uploaded issue #1266

CLAUDE.md

@@ -0,0 +1,126 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project overview
+
+aNCA is an R package providing a Shiny app for automated Non-Compartmental Analysis (NCA) on pre-clinical and clinical pharmacokinetic data. It builds on `PKNCA` (>= 0.12.1) as the core NCA engine and produces CDISC outputs (ADNCA, PP, ADPP), configurable TLGs, and slide decks.
+
+**Read `AGENTS.md`** — it is the single source of truth for all conventions, code principles, and anti-patterns. The sections below only add what AGENTS.md doesn't already cover.
+
+## Build and test commands
+
+```r
+devtools::load_all()        # Load package in development
+devtools::document()        # Rebuild NAMESPACE + man/ after roxygen changes
+devtools::test()            # Run all unit tests
+devtools::test_active_file()# Run current test file only
+devtools::check()           # Full R CMD check
+lintr::lint_package()       # Code style check
+styler::style_file("R/foo.R") # Format a file to tidyverse style
+```
+
+To launch the Shiny app: `aNCA::run_app()` — automatically loads test data on startup. Set `aNCA_LOG_LEVEL="TRACE"` in `.Renviron` for debug logging.
+
+CI runs on every PR via GitHub Actions: lintr, spelling, R CMD check, test coverage, and documentation validation.
+
+## Two code zones
+
+**`R/`** — Package API. Functions usable without the Shiny app. Exported functions live here with full roxygen2 docs. No `library()`/`require()` allowed. Imports used via `@importFrom`, Suggests used via `pkg::fun()`.
+
+**`inst/shiny/`** — Shiny application. `app.R` is the entry point, `modules/` contains the tab-level UI+server modules, `functions/` holds app-only helpers (auto-sourced by app.R). Code here can use `require()` since it runs inside the Shiny process.
+
+## Shiny data flow
+
+```
+data_upload_server → adnca_raw (reactive) → tab_data_server → tab_nca_server
+                                                                    ↓
+                                              processed_pknca_data → tab_tlg_server
+```
+
+Module communication uses `session$userData`:
+- `session$userData$results` — CDISC datasets and NCA results
+- `session$userData$project_name()` — reactive, auto-populated from STUDYID
+- `session$userData$slope_rules()` — reactive
+- `session$userData$settings_versions` — versioned YAML settings list
+
+## Tab structure
+
+| Tab | Module file | Purpose |
+|-----|------------|---------|
+| Data | `tab_data.R` + `tab_data/` | Upload, mapping, filtering, data preprocessing |
+| Exploration | `tab_explore.R` + `tab_explore/` | Interactive plots (line, boxplot, PK/Dose QC) |
+| NCA | `tab_nca.R` + `tab_nca/` | NCA settings, parameter selection, slope selector, ratios, exclusions, results |
+| TLG | `tab_tlg.R` + `tab_tlg/` | Tables/listings/graphs defined in `inst/shiny/tlg.yaml` |
+| About | `tab_about.R` | Citations, session info, app version |
+
+## Exports and ZIP
+
+Export workflow in `tab_nca/zip.R`: `TREE_LIST` defines export structure. Selected items come from `input$res_tree`. ZIP filename uses project name or falls back to `NCA_STUDYID.zip`. Pre-Specs sheets are auto-generated from CDISC data.
+
+## Styling (CSS/SCSS)
+
+Styles authored in `inst/shiny/www/styles/` SCSS partials, compiled to `main.css`. Entry point: `styles/main.scss`. When editing styles, modify the `.scss` partial **and** apply the same change to `main.css` (the R compile script may not be available). Sidebar width is `--_sidebar-width: 170px !important` in `main.css`.
+
+## Exploration plots conventions
+
+- Default `color_by` priority: `DOSEA > TRT01A > GROUP > ACTARM > COHORT`
+- Default `facet_by` priority: `TRT01A > DOSEA > GROUP > ACTARM > COHORT`
+- Auto-mapping includes: `COHORT`, `PART`, `PERIOD`
+
+## Color constants
+
+- **SCSS variables**: `inst/shiny/www/styles/modules/_colors.scss`
+- **R constants**: `inst/shiny/functions/colors.R` (auto-sourced, available in all Shiny modules)
+- **Exclusion colors**: `inst/shiny/functions/utils-exclusions.R` — `EXCL_COLOR_NCA`, `EXCL_COLOR_TLG`, `EXCL_COLOR_BOTH`, `EXCL_COLOR_PARAM`
+- **Flag colors**: `inst/shiny/modules/tab_nca/nca_results.R` — `FLAG_COLOR_FLAGGED`, `FLAG_COLOR_MISSING`
+
+## Imputation pipeline
+
+BLQ (Below Limit of Quantification) and start concentration (C0) imputation spans multiple files:
+
+| Step | File | Key function |
+|------|------|-------------|
+| UI | `inst/shiny/modules/tab_nca/setup/data_imputation.R` | `data_imputation_server()` — returns `blq_imputation_rule`, `impute_c0`, `blq_strategy` |
+| Settings assembly | `inst/shiny/modules/tab_nca/setup/settings.R#452-491` | `settings()` reactive — bundles `data_imputation` into the settings list |
+| Data object update | `R/PKNCA.R#297` | `PKNCA_update_data_object(start_impute, blq_imputation_rule)` |
+| Interval imputation | `R/intervals.R#215` | `update_main_intervals(impute, blq_imputation_rule)` — sets `data$intervals$impute` column |
+| Start impute | `R/create_start_impute.R` | `create_start_impute()` — adds C0 strategies (`start_conc0`, `start_predose`, `start_logslope`, `start_c1`) |
+| BLQ global function | `R/PKNCA.R#439` | `PKNCA_calculate_nca(blq_rule)` — registers `PKNCA_impute_method_blq` globally before calling `PKNCA::pk.nca()` |
+| Obs param cleanup | `R/intervals.R#326` | `rm_impute_obs_params()` — removes imputation from non-AUC-dependent parameters |
+
+### Critical guard
+
+`update_main_intervals()` must ensure `data$intervals$impute` exists **before** the BLQ `dplyr::mutate()` block. If the column is missing and `impute` is also a function parameter (e.g. `FALSE` from YAML `impute_c0: no`), dplyr resolves to the parameter, producing `"blq, FALSE"` which PKNCA interprets as a lookup for `PKNCA_impute_method_FALSE`. The guard `if (!"impute" %in% names(data$intervals))` (see `rm_impute_obs_params()` line 341) prevents this.
+
+## Interval parameter helpers
+
+- **`rename_interval_params()`** (`R/utils.R:17`): Appends `_start-end` suffix to PPTESTCD for manual interval params (e.g. `AUCINT` → `AUCINT_0-24`). Called in `descriptive_statistics.R`, `parameter_plots.R`, `flexible_violinboxplot.R`.
+- **`parse_interval_parameter()`** (`R/ratio_calculations.R:326`): Reverses the above — extracts `base`, `start`, `end`, `is_interval` from a suffixed name. Used when labels need to be resolved from `metadata_nca_parameters` (which only stores base PPTESTCDs).
+
+## YAML boolean caveat
+
+R's `yaml` package parses YAML 1.1 booleans: `yes`/`no`/`true`/`false`/`on`/`off` all become R logical values. When settings YAML values like `impute_c0: no` are parsed, they become logical `FALSE`, not the string `"no"`. Code that passes these values into `if()` conditions or dplyr expressions must handle logical values correctly — prefer `isTRUE()` / `isFALSE()` guards over bare `if (value)` when the value may be logical from YAML.
+
+## Testing conventions
+
+- Test files: `tests/testthat/test-<source>.R`, matching source file name
+- Use `describe()` / `it()` blocks with value-level assertions
+- Test data created in `tests/testthat/setup.R` and `tests/testthat/data/`
+- E2E tests in `test-e2e-runner.R` use `shinytest2` (in Suggests)
+
+## Package versioning and release
+
+- Semantic versioning. Bump `DESCRIPTION` version (+1 from main) for non-trivial changes
+- `{admiral}` family follows quarterly releases (Mar/Jun/Sep/Dec); aNCA extensions should align within 2 weeks
+- `NEWS.md` entries reference PR numbers
+
+## PR workflow summary
+
+1. `git fetch origin main && git checkout origin/main` — branch from latest upstream
+2. Branch name: `<issue-number>-<type>/<short-description>`
+3. After code changes: `document()` → `lint_package()` → `test()` → `check()`
+4. Update `NEWS.md`, bump `DESCRIPTION` version
+5. Push to fork, create PR against `pharmaverse/main`
+6. Add 2+ reviewers from DESCRIPTION authors
+7. Never force-push; use separate commits instead of amending

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9173
+Version: 0.1.0.9174
 Authors@R: c(
     person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
            comment = c(ORCID = "0009-0001-1626-1526")),

NEWS.md

@@ -79,6 +79,7 @@
 * DOSNOA computation fixed for specimen-level grouping — urine-only data no longer gets incorrect dose numbering (#1116)
 * Dose-aware AUCint parameters now share the same PPTESTCD as their non-dose-aware counterparts in CDISC exports, with `PPANMETH` indicating the analytical method. Internal PPTESTCDs renamed from misleading `D` suffix (e.g. `AUCINTD`) to lowercase `da` suffix (e.g. `AUCINTda`). Fixed wrong PPTEST label for `AUCINTD` which said "Normalized by Dose" (#1242)
 * Optional settings (`slope_rules`, `int_parameters`, `ratio_table`) are now normalized to `NULL` when empty, instead of persisting as 0-row data frames throughout the app and settings pipeline (#1262)
+* Fixed `PKNCA_impute_method_FALSE` error when YAML settings contain `impute_c0: no` — the `impute` column is now initialized before BLQ imputation is applied to prevent dplyr from resolving to the boolean function parameter (#1266)
 * Interval-specific parameters (`aucint.*`, `cav.int.*`) excluded from the Parameter Selection matrix — they require finite sub-intervals and must be configured via Partial Interval Calculations (#1309)
 
 ### Ratio Calculations

R/intervals.R

@@ -290,6 +290,13 @@ update_main_intervals <- function(
     data <- create_start_impute(data)
   }
 
+  # Ensure impute column exists so dplyr mutate below references the column
+  # rather than the function parameter (which could be FALSE from YAML settings,
+  # causing "PKNCA_impute_method_FALSE" not found error).
+  if (!"impute" %in% names(data$intervals)) {
+    data$intervals$impute <- NA_character_
+  }
+
   ############################################
   # Define a BLQ imputation method for PKNCA
   # and apply it only for non-observational parameters