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Changelog

Source: NEWS.md

aNCA (development version)

Bug fixes

  • 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)

Features added

<<<<<<< 728-enhancement/remove-bioavailability-special-case * Removed dedicated bioavailability calculation pipeline — FABS/FREL are now computed exclusively via the ratio calculations table (#1260) ======= * Added pkgdown vignette documenting all ratio calculation types: metabolite ratios, accumulation ratios, renal clearance, absolute/relative bioavailability, and generic ratios (#1251) >>>>>>> main * Ratio Calculations UI replaced with formula-style cards showing PPTESTCD = Test [Group] / Ref [Group] × Factor layout (#1250) * Parameter Exclusions: exclude individual PK parameter rows from descriptive statistics and ADPP export via PPSUMFL/PPSUMRSN flags (#1040) * Partial Interval Calculations table now starts empty by default and includes a (-) Remove Row/s button matching the Ratio Calculations style (#1249) * Settings upload now auto-restores the previous session: auto-applies mapping, filters, and data processing, navigates to the saved tab, and auto-runs NCA if it was previously run. Incompatible settings degrade gracefully with user notifications (#1225) * Added dose-normalised slides to the PPT/QMD export. Each group now includes an optional “Dose-Normalized Plots” summary slide (dose-normalised mean plot + parameter table) and an optional “Dose-Normalized PK Parameters” individual slide. Both are controlled via the Customize Slides modal and default to CMAXD, AUCLSTD, and AUCIFOD (#1054). * Interval/partial parameters (e.g. AUCINT_0-20) are now selectable in the ratio calculations Test/Ref Parameter dropdowns, with correct start/end filtering in the ratio computation (#1135) * run_app() now accepts a settings parameter to pre-load a YAML settings file on startup (#514) * Exploration sidebars: “View Exports” button opens a scrollable gallery modal showing all saved plots inline with name, type, timestamp headers and a remove option (#1137) * Added “Min. Points for Half-life” setting in NCA > Settings > General Settings, allowing users to configure PKNCA’s min.hl.points option (range 2–10, default 3) (#1155) * Settings version control: single YAML file stores multiple versions with metadata (timestamp, comment, dataset, aNCA version, active tab). Save button in header, version selection modal on upload, version delete support (#1103) * ADPP now includes CRITy/CRITyFL columns for each checked flag rule and PPSUMFL/PPSUMRSN columns indicating summary exclusion status. Flagged records are excluded from descriptive statistics and parameter plot statistics, with an optional toggle to overlay excluded points as crosses (#1141) * Right-side sidebars (Exploration, NCA Parameter Plots, TLG) can now be resized by dragging the left edge. Default width increased to 250px, left nav sidebar reduced to 150px (#1156) * Moved rlistings, officer, and flextable from Imports to Suggests with user-facing notifications when missing (#1106) * Save button is now enabled after data mapping with progressive content: exploration plots and settings before NCA, full export after NCA (#1136) * General Exclusions: “Excl. TLG” checkbox per exclusion entry sets PKSUM1F to “Y”, filtering those rows from TLGs (#1018) * NCA Setup filter pickers reordered to Analyte, Specimen, NCA Profile with bidirectional cascading updates between Analyte and Specimen (#1114) * Column mapping is now included in settings YAML export and restored on upload, with validation against available columns (#1104) * Ratio calculations table is now included in settings YAML export and restored on upload, with validation against available parameters and groups (#1091) * Data tab filters are now included in the settings YAML file and restored on upload, for both standalone settings download and ZIP export (#1082) * Non-standard grouping variables (chosen in the data mapping) are now included as columns in ADPP and ADNCA outputs (#1077) * Searchable PK parameter reference table added to NCA > Setup, showing metadata, app location, and PKNCA function for each parameter (#1023) * Settings YAML units can now contain just PPTESTCD and PPSTRESU (default target units). (#1027) * Exploration plots: toggle legend visibility, improved tooltips with color-by variable, and correct axis/legend labels (#988) * Exploration plots: “Add to Exports” button saves named plot snapshots to the ZIP export. When custom snapshots exist for a plot type, only the snapshots are exported (the default plot is omitted). QC plot also included in the export tree (#1002) * CDISC ZIP export now includes a Pre_Specs.xlsx file with variable-level metadata for each selected dataset (#998) and a session information file (#829) * New “About” tab in the app sidebar with links, citation, authors, license, version info, and a “Copy session info” button (#1015) * Export filenames use STUDYID as fallback when no project name is set, date suffix removed (#1000) * Project name auto-populated from STUDYID on data upload (#1000) * Enhancements to the slides outputs including grouping by PKNCA groups, dose profile, and additional grouping variables (#791) * Option to include and apply NCA flag rules with reasons (NCAwXRS) as defined by ADNCA standards. Any record populated within these columns will be excluded for the NCA (#752) * R script exported in ZIP folder to re-run and replicate App outputs (#789) * Individual and Mean plots tabs now created using the same function, so the layout and plot themes are consistent across both plots (#712) * New flagging rule for lambda-z calculations based on r-squared, R2 (#834) * New Parameter Selection section in NCA tab allowing to select parameters by study type (#795) * The App optionally maps end of sample collection (AEFRLT) for excretion rate parameter calculations: ERTLST, ERTMAX. (#745) * Option to upload multiple input files, which will be bound together to form a single ADNCA data set (#821) * BLQ imputation rules can be applied to the NCA via NCA Setup > Data Imputation (#139) * Section General Exclusions allowing to perform in-App NCA exclusions (#851) * Mean plots have been added in the TLGs section, with BLQ handling (#555) * CMAX automatically selected in box plots if available (#890) * Allow user to select additional grouping variables (chosen in the mapping) for ratio calculations (#868) * General button at top page to save all NCA results, settings & draft slides as a ZIP file (#638) * Settings are now uploaded on initial opening of the app in the data tab, and applied to the next steps (#860) * Settings file has been converted from rds to yaml, allowing better readability and editing for users. (#901) * WTBL and WTBLU columns added to the data mapping, for optional conversion of dose to adjust to body weight for excretion calculations (#959) * Slope selector table for half life adjustments uses time to choose the point of interest. Also it is aesthetics have been polished (#956) * Partial interval parameters section now allows other calculations than AUCINT, such as RCAMINT, AUCINTD or CAVGINT among others (#524) * Slope selector plots count with grouping options (#333) * Add x/y axis limits for the exploration plots (#817) and facet titles including subject count (#894) * Settings upload and processing is flexible, so non-data specific template settings can be uploaded (#993) * Mapping will allow custom numeric input values instead of columns for ADOSEDUR and TRTRINT (#1051) * Help buttons have been included/updated for most App sections: Parameter Selection, Slope Selector, Additional Analysis and Partial Interval calculations (#975) * Removed methods, scales, and stringr from package dependencies, replacing all usages with base R equivalents (#1108) * SelectInputs updated using a new function to ensure all widgets include variable labels. (#899) * Export modal now allows users to select which slide sections (mean plots, statistics, line plots, box plots, individual plots/parameters, additional analysis) to include in PPTX and HTML exports; box plot parameters are also configurable (#972) * Settings file now outputs and time duplicate exclusions and processes them automatically upon settings upload (#1195) * Parameter selection UI replaced with an interactive checkbox matrix (study types × parameters). Includes Select all, Defaults, and Clear all buttons.

Bugs fixed

  • Fixed ratio calculations with Aggregate Subject = yes or if-needed not aggregating reference values, and ratio parameter columns (FABS, FREL, etc.) not appearing in NCA Results (#1273)
  • Last dose interval end time now extends to the last observed sample instead of being cut off at TRTRINT (tau), ensuring all collected data points are included in NCA calculations (#1235)
  • Fixed NA PPSTRESU handling across NCA results: descriptive statistics no longer crash when a parameter group has all-NA units, and manual interval parameters (e.g., RCAMINT) no longer get NA appended to their column names (#1216)
  • get_settings_code() now reads mapping, filters, ratio table, and units from the settings YAML instead of using hardcoded defaults. Legacy YAML files without these fields still work via fallback. The mapping parameter has been removed (#1189)
  • SASS compilation moved from runtime (app.R) to a data-raw/compile_css.R script, fixing startup crashes on read-only deployments (#1107)
  • ZIP folder with results will now include the exploration tab outputs: individual plots, mean plots (#794)
  • Updated TMAX label from Time of CMAX to Time of CMAX Observation (#787)
  • Bug fix for box/violin plots that were crashing when violin option selected (#786)
  • Summary statistic table changes in grouping variables won’t remove previous summary settings (#840)
  • No longer offering direct PK calculations for renal clearance (RENALCL) parameters. PKNCA is currently inaccurate. Instead, the ratios table should be used (#781)
  • No longer offering PK calculations for PKNCA multidose parameters; mean residence time (MRTMDO, MRTMDP), steady state volume of distribution (VSSMDP, VSSMDO) and time above (TAT). They are not really able to be calculated using PKNCA (#869)
  • Bug fix for settings upload via zip file output (#832)
  • Bug fix for plotting section where if there is >1 unit the axis label will contain both unique units. (#818)
  • Units table bugs fixed, so it is filtered based on NCA setup and the table is searchable for each column (#870)
  • Bug fix to allow for unrecognized units to be used in AVALU and DOSEU (#861)
  • Bug fix so NA units are allowed in the data (as per CDISC guidelines for NA samples) and not treated as a unique unit (#907)
  • Bug fix so app doesn’t crash if NCA is rerun with an error (e.g. No exclusion REASON) (#913)
  • NCA results flagging logic updated to include Missing column and correctly identify difference between missing and not requested (#934)
  • Pagination controls in the slope selector and the interactivity of the plots is less buggy (#956)
  • Creation of intervals reworked to prevent doses being combined if no samples are taken post dose (#963)
  • Parameter selection no longer resets after changes to NCA setup and slope selector- apart from changes to analyte and pcspec that change the study types detected (#1008)
  • Prevent a crash when selecting already defined identity variables (i.e, DOSETRT) for the Additional Grouping Variables in the Mapping Tab (#1060)
  • Filtering will now correctly also affect all the input widgets in NCA setup (#1092)
  • All Results input widgets now shows each manual interval parameter with its range suffix (e.g. AUCINT_0-12, CAVGINT_0-24) instead of collapsing them into a single entry (#1146)
  • Boxplot parameter selector and excretion end time column selector now restrict to single selection, preventing errors when downstream code expects a single value. Boxplot selector also shows each manual interval parameter with its range suffix (e.g. AUCINT_0-12, CAVGINT_0-24) instead of collapsing them into a single entry (#1148)
  • Manual interval parameter renaming now uses dose-relative times (start_dose/end_dose) consistently across descriptive statistics, parameter plots, and boxplots, matching pivot_wider_pknca_results (#1169)
  • Descriptive statistics parameter columns are now correctly displayed when using the selector_label widget, and duplicate rows from the concentration data join are deduplicated (#1169)
  • Fixed PKNCA_update_data_object custom units table join using hardcoded by = c("PPTESTCD", "PPORRESU") instead of dynamic keys, which failed when the units table included group columns like PARAM or PCSPEC (#1159)
  • Fixed DOSNOA computation using specimen-level grouping (including PCSPEC/PARAM), causing urine-only Day 10 data to get DOSNOA=1 instead of DOSNOA=2, leading to incorrect dose time matching (#1116)
  • Fixed “Summarise by” selector in Matrix Ratios having no effect due to input ID mismatch (summarygroups vs summary_groups) (#1198)

aNCA 0.1.0

CRAN release: 2025-12-09

  • Initial CRAN submission.