Mean concentration plots no longer drop timepoints that are well under the BLQ threshold: the BLQ ratio counted flagged records against a denominator of distinct subjects, so a subject contributing several records to a timepoint could push the ratio above 1. It is now counted per subject on both sides (#1356)
The “X ticks” option on the linear and logarithmic concentration plots now takes effect. plotly was regenerating the axis itself, so the chosen column was ignored; the side-by-side variants were already unaffected (#1356)
Mean concentration plots (pkcg03) and the urine, dose-proportionality and box plot entries no longer render as blank panels: graph output IDs were taken from the plot list’s names while the render bindings were registered by position, so any TLG whose plots are split into a named list never bound to its output. Split graphs now also show the group as a header, the way split tables do (#1356)
TLG sidebar options set to 0 are no longer silently ignored: the option filter treated a literal 0 the same as “unset”, so an axis limit of 0 (xmin/ymin) had no effect (#1356)
A TLG that produces no output now explains why instead of rendering a blank panel with no message (#1356)
Combined concentration plots (pkcg02) no longer group by USUBJID by default, which produced one plot per subject instead of an overlaid combined plot. They now default to the study’s PKNCA grouping variables (which exclude the subject), with USUBJID still available as an explicit choice; the individual side-by-side plot (pkcg01) correspondingly groups by subject rather than by treatment (#1356)
Concentration plot titles no longer disappear when a plot group covers more than one treatment: the treatment names are now collapsed into a single subtitle string, where previously the subtitle became a character vector that plotly rendered as no title at all (#1356)
Concentration plot subtitles no longer mislabel grouping variables: a variable with no configured display name (e.g. USUBJID on pkcg02) is labeled with its own name instead of being dropped, which shifted every following label onto the wrong value (#1356)
The pkcg03 mean plot “Summary Statistic” dropdown now opens with its default (Mean_sdi) selected instead of appearing blank (#1356)
Fix app failing to launch from an installed package: internal (non-exported) functions called from the Shiny app are now namespace-qualified so they resolve after R CMD INSTALL, and the app logo is served from inst/shiny/www/ instead of the non-installed man/figures/ (#1378)
Testing
Add 100% line coverage for g_pkcg.R, g_lineplot.R, l_pkcl01.R, and TLG Shiny modules (#1351)
Features
TLG Catalog
Implement new TLG functions to complete the pkct01, pkpt03/07/08/11, pkpg01/02/03/04/06, pkpl01/04, and pkcl02 catalog entries (#1343):
t_pkct01 / t_pkct01_dose / t_pkct01_tad / t_pkct01_dose_tad — summary concentration tables (by TRT or dose, from first dose or TAD)
t_pkpt03_col / t_pkpt03_MP_col — PK parameter summary tables with stats in columns (full dataset and metabolite/parent filtered)
l_pkpl04_mp — individual PK parameter listing organised for treatment comparison
l_pkcl02_uri — urine concentration and volume listing
ADPP-based TLG outputs now correctly exclude rows flagged via PPSUMFL = "Y", consistent with ADNCA exclusion via PKSUM1F (#1343)
Summary tables are easier to read: split tables (e.g. by analyte/specimen) now show the group as a header, t_pkct01 rows are grouped by treatment arm with timepoints in numeric order, statistic columns use readable headers (e.g. “Geometric Mean”, “CV%”), and urine specimen filtering matches PCSPEC/PPSPEC case-insensitively (#1343)
The new TLG tables and listings expose right-sidebar customization options (grouping/stratification variables, displayed columns, titles, and filters) matching the original l_pkcl01 listing; stratification variables are selectable so summary tables can be grouped by covariates such as SEX or RACE (#1356)
Summary-exclusion flags are scoped both to summary outputs and to their own dataset: ADNCA (concentration) outputs filter on PKSUM1F and ADPP (PK parameter) outputs on PPSUMFL, so a record excluded from one summary is not dropped from the other’s TLGs, and individual listings show all records (matching their “subjects excluded from the summary table” footnote) (#1356)
Summary tables can compare covariate groups side by side: a new “Compare in columns” option on the pkct01 and pkpt03/07/08 tables repeats the statistic block per level of a chosen variable (e.g. SEX, RACE), rendered as a two-level Group × Statistic column header (#1356)
Summary tables let you choose which statistics to display: a new “Statistics to show” option on the pkct01 and pkpt03/07/08 tables filters the columns (e.g. n, Number BLQ, Mean, SD, CV%); leaving it empty shows all statistics as before (#1356)
Summary-table sidebar inputs share one layout: every summary table (pkct01 variants and pkpt03/07/08) exposes the same option groups — Filtering, Grouping (Split / Stratify), Value, Compare, and Statistics — with PARAM and the time/visit columns selected within “Stratify by (rows)” rather than through separate inputs. “Stratify by (rows)” is a multi-select on all of them; on the pkpt tables it defaults to every PKNCA grouping variable except the subject (USUBJID) so statistics separate by treatment, parameter, and specimen out of the box. The pkpt11 GMR table keeps its comparison-specific inputs as a documented exception (#1356)
The urine-only TLGs (pkpt08, pkcl02) restrict their specimen filter to values that look like urine, selected by default, so a urine table or listing cannot be pointed at serum or plasma while non-standard labels such as “Urine - void” stay selectable (#1356)
Split-table group headers name the variable as well as the value (e.g. “PPCAT: Drug A / PCSPEC: PLASMA”) so stacked outputs are self-describing, and summary tables warn when a stratification variable is dropped for also being a table-split variable (#1356)
The standalone mean, urine, dose-proportionality and box plot entries (pkcg03 by dose, pkpg01/pkpg02/pkpg03/pkpg04/pkpg06) expose Title, Subtitle and Footnote inputs in the sidebar, matching the other graph entries (#1356)
Summary tables can filter which stratification values appear: a “Parameters to show” filter on the pkpt03/07/08 tables and a “Timepoints to show” filter on the pkct01 tables restrict the rows to the chosen PARAM/timepoint values (#1356)
Summary tables now warn (instead of silently degrading) when a chosen stratification variable is not present in the data — e.g. the “by Dose” concentration tables when a dose-amount column is not carried in the concentration data — so it is clear why a table grouped by fewer variables (#1356)
Settings & Configuration
Settings upload auto-restores the full session: mapping, filters, data processing, tab navigation, and auto-runs NCA if previously run. Incompatible settings degrade gracefully with notifications (#1225)
Settings version control: YAML file stores multiple versions with metadata. Save button in header, version selection on upload, version delete support (#1103)
Settings file converted from RDS to YAML for readability and manual editing (#901)
Settings are uploaded on initial opening of the app in the data tab and applied to the next steps (#860)
Column mapping, data filters, ratio table, units, and time-duplicate exclusions are now included in settings YAML export/import (#1082, #1091, #1104, #1195)
run_app() accepts a settings parameter to pre-load a YAML settings file on startup (#514)
Settings upload is flexible — non-data-specific template settings can be uploaded (#993)
Exploration
“Copy Plot Code” button in the right sidebar opens a modal with a self-contained R script for the current plot, including data loading, mapping, filtering, and PNG/HTML export (#1327)
NCA Setup
Renamed “Aggregate Subject” label to “Mean across subjects” in ratio calculations for clarity; updated help text to explain matching mechanics (#1297)
Parameter Selection tab now contains Partial Intervals, Ratio Calculations, and Units alongside the parameter matrix. The former Settings tab is renamed to General Settings (#1239)
Parameter selection UI replaced with an interactive checkbox matrix (study types × parameters) with Select All, Defaults, and Clear All buttons (#795)
Partial interval parameters section supports calculations beyond AUCINT: RCAMINT, AUCINTD, CAVGINT, and others. Table starts empty by default with a Remove Row button (#524, #1249)
X/Y axis limits for exploration plots, facet titles with subject count (#817, #894, #984)
Individual and Mean plots use the same function for consistent layout and themes (#712)
Right-side sidebars resizable by dragging; default width 250px (#1156)
Export & Output
PowerPoint export includes a PPTESTCD glossary slide after the title slide, listing all PK parameter codes and their full names (#1326)
General button at top of page to save all NCA results, settings, and draft slides as a ZIP file (#638)
Dose-normalised summary slides added to PPT/QMD export, controlled via Customise Slides modal (#1054)
Export modal allows selecting which slide sections to include in PPTX/HTML exports (#972)
CDISC ZIP includes Pre_Specs.xlsx with variable-level metadata and session info (#998, #829)
ADPP includes CRITy/CRITyFL columns for flag rules and PPSUMFL/PPSUMRSN for summary exclusion status (#1141)
Non-standard grouping variables included in ADPP and ADNCA outputs (#1077)
R script exported in ZIP to replicate app outputs (#789)
Save button enabled after data mapping with progressive content (#1136)
Export filenames use STUDYID as fallback; project name auto-populated from STUDYID (#1000)
Slide outputs grouped by PKNCA groups, dose profile, and additional grouping variables (#791)
Mean plots added to TLGs section with BLQ handling (#555)
CMAX auto-selected in box plots if available (#890)
Data & Mapping
ADNCA now includes PKSUM1RS column storing the general exclusion reason when PKSUM1F = "Y" (#1331)
Upload multiple input files, bound into a single ADNCA dataset (#821)
Optional mapping of AEFRLT for excretion rate parameters (ERTLST, ERTMAX) (#745)
WTBL/WTBLU columns for dose-to-body-weight conversion in excretion calculations (#959)
Custom numeric input values for ADOSEDUR and TRTRINT instead of column mapping (#1051)
SelectInputs updated to include variable labels (#899)
Documentation & UI
UI consistency pass: standardized dropdown labels to “Select the…”, help button placement to right-aligned, “colour” to “color”, renamed Save to “Export as ZIP”, simplified download button text, and added “Short Parameter”/“Specimen” columns to Units table (#1333)
Searchable PK parameter reference table in NCA > Setup (#1023)
R Script Walkthrough vignette added to pkgdown website (#1090)
Ratio Calculations vignette documenting all ratio types (#1251)
“About” tab with links, citation, authors, license, version, and “Copy session info” button (#1015)
Help buttons added/updated for Parameter Selection, Slope Selector, Additional Analysis, and Partial Interval Calculations (#975)
Slope selector table uses time-based selection with improved aesthetics and grouping options (#956, #333)
Bug fixes
Data & Mapping
The “Next” button in the Data tab is no longer permanently disabled after an incomplete-mapping error. Users can now correct the mapping and continue without restarting the app (#1402)
CDISC Export
CRITxFL now uses "" instead of "N" when criterion is violated. CRITx shows the acceptance criterion with inverted operator (e.g. flag rule R2ADJ < 0.7 produces CRITx = "R2ADJ >= 0.7"). CRITxFL = "Y" means criterion satisfied (#1332)
NCA Calculations
Renal clearance (RENALCL) removed from direct PK calculations (inaccurate in PKNCA) — use ratio table instead (#781)
Multidose parameters (MRTMDO, MRTMDP, VSSMDO, VSSMDP, TAT) removed from direct calculations (#869)
Last dose interval end time extends to last observed sample instead of being cut off at tau (#1235)
Interval creation reworked to prevent doses being combined when no post-dose samples exist (#963)
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)
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
Fixed Aggregate Subject = yes/if-needed not aggregating reference values, and ratio columns not appearing in results (#1273)
NCA Results & Export
Interval parameters (e.g. AUCINT_0-24) now display human-readable labels in parameter selectors and boxplot y-axis, instead of raw PPTESTCDs (#1305)
Descriptive statistics were silently ungrouped when exported before visiting the tab — now falls back to default grouping columns (#1264)
Fixed NA PPSTRESU handling: descriptive statistics no longer crash on all-NA unit groups, and manual interval parameters no longer get NA in column names (#1216)
get_settings_code() reads mapping, filters, ratio table, and units from YAML instead of hardcoded defaults (#1189)
All Results widgets show interval parameters with range suffix (e.g. AUCINT_0-12) instead of collapsing into one entry (#1146)
Interval parameter renaming uses dose-relative times consistently across statistics, plots, and boxplots (#1169)
NCA results flagging correctly distinguishes missing vs not-requested parameters (#934)
Custom units table join uses correct keys instead of hardcoded columns (#1159)
“Summarise by” selector in Matrix Ratios fixed (input ID mismatch) (#1198)
export_cdisc() now includes ATPTREF and ROUTE columns in ADPP output (#1276)
Slope selector
Slope Selector plots are rendered again without error Can't transform a data frame with NA or '' names when a grouping value (e.g. STUDYID, PARAM) contains an underscore. Plot names are now parsed at key= boundaries instead of splitting on every underscore (#1378).
Settings & Upload
SASS compilation moved from runtime to build-time script, fixing startup crashes on read-only deployments (#1107)
ZIP export includes exploration tab outputs: individual and mean plots (#794)
Box/violin plots no longer crash when violin option selected (#786)
Boxplot parameter selector restricted to single selection; shows interval parameters with range suffix (#1148)
Axis labels show both unique units when >1 unit exists (#818)
Units & Data
Units table filtered based on NCA setup; searchable per column (#870)
Unrecognized units allowed in AVALU and DOSEU (#861)
NA units allowed in data per CDISC guidelines (#907)
TMAX label corrected from “Time of CMAX” to “Time of CMAX Observation” (#787)
Pagination controls in the slope selector are less buggy (#956)
TLG
Fixed one-sided whiskers (Upper/Lower) collapsing to zero height in mean plots (pkcg03) (#1316)
Fixed TLG graph title/label handling: custom titles now apply immediately to combined graphs (pkcg02) via dedicated plotly outputs, and the !COLUMN label-reference syntax works again across title, subtitle, footnote, and axis inputs (column labels are re-applied before rendering, since the PKNCA pipeline strips them) (#1336)
Dependency changes
Removed tern and nestcolor — TLG plots (pkcg01, pkcg02, pkcg03) now use inline ggplot2 code (#1316)
rlistings, officer, and flextable moved from Imports to Suggests — the app notifies users when these are missing (#1106)
Removed methods, scales, and stringr from package dependencies, replaced with base R equivalents (#1108)
Settings YAML units accept minimal format: just PPTESTCD and PPSTRESU (#1027)