Enhancement/Expansion of TLG Catalog

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9177
+Version: 0.1.0.9179
 Authors@R: c(
     person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
            comment = c(ORCID = "0009-0001-1626-1526")),

NAMESPACE

@@ -42,10 +42,13 @@ export(format_pkncadose_data)
 export(g_lineplot)
 export(g_pkcg01_lin)
 export(g_pkcg01_log)
+export(g_pkcg01_sbs)
 export(g_pkcg02_lin)
 export(g_pkcg02_log)
+export(g_pkcg02_sbs)
 export(g_pkcg03_lin)
 export(g_pkcg03_log)
+export(g_pkcg03_sbs)
 export(generate_pre_specs)
 export(generate_tooltip_text)
 export(get_conversion_factor)
@@ -55,7 +58,21 @@ export(get_settings_code)
 export(interval_add_impute)
 export(interval_remove_impute)
 export(l_pkcl01)
+export(l_pkcl01_tad)
+export(l_pkcl02_uri)
+export(l_pkpl01)
+export(l_pkpl01_mp)
+export(l_pkpl04_mp)
 export(multiple_matrix_ratios)
+export(p_pkcg03_lin_dose)
+export(p_pkcg03_log_dose)
+export(p_pkcg03_sbs_dose)
+export(p_pkpg01_cum)
+export(p_pkpg01_per)
+export(p_pkpg02_doseprop)
+export(p_pkpg03_boxp)
+export(p_pkpg04_boxp)
+export(p_pkpg06_mp)
 export(parse_annotation)
 export(pivot_wider_pknca_results)
 export(pk.calc.ermax)
@@ -73,6 +90,15 @@ export(remove_pp_not_requested)
 export(run_app)
 export(settings_version_summary)
 export(simplify_unit)
+export(t_pkct01)
+export(t_pkct01_dose)
+export(t_pkct01_dose_tad)
+export(t_pkct01_tad)
+export(t_pkpt03_MP_col)
+export(t_pkpt03_col)
+export(t_pkpt07_norm)
+export(t_pkpt08_uri)
+export(t_pkpt11_gmr)
 export(translate_terms)
 export(update_main_intervals)
 export(write_versioned_settings)
@@ -124,10 +150,15 @@ importFrom(dplyr,where)
 importFrom(formatters,`var_labels<-`)
 importFrom(formatters,var_labels)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_errorbar)
+importFrom(ggplot2,geom_jitter)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplot_build)
 importFrom(ggplot2,ggplot_gtable)
@@ -137,6 +168,10 @@ importFrom(ggplot2,scale_color_viridis_d)
 importFrom(ggplot2,scale_colour_manual)
 importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_log10)
+importFrom(ggplot2,scale_y_log10)
+importFrom(ggplot2,stat_summary)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(glue,glue)
 importFrom(grid,convertUnit)
@@ -160,6 +195,7 @@ importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
 importFrom(reactable,reactable)
 importFrom(reactable.extras,reactable_extras_dependency)
+importFrom(rlang,.data)
 importFrom(rlang,expr)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
@@ -169,11 +205,14 @@ importFrom(shinycssloaders,withSpinner)
 importFrom(shinyjqui,orderInput)
 importFrom(shinyjs,useShinyjs)
 importFrom(stats,as.formula)
+importFrom(stats,coef)
+importFrom(stats,confint)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stats,qt)
+importFrom(stats,quantile)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(tidyr,crossing)

NEWS.md

@@ -6,6 +6,23 @@
 
 ## 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)
+  - `t_pkpt07_norm` — dose-normalized PK parameter summary table
+  - `t_pkpt08_uri` — urine cumulative amount and % dose recovered summary table (n, Mean, SD, CV%, Median, Min, Max)
+  - `t_pkpt11_gmr` — geometric mean ratio table with 90% CIs
+  - `p_pkpg03_boxp` / `p_pkpg04_boxp` — boxplots of primary PK parameters (with and without individual data points)
+  - `p_pkpg06_mp` — boxplot of metabolite/parent PK parameter ratios
+  - `p_pkpg01_cum` / `p_pkpg01_per` — mean cumulative urine amount and % dose recovered line plots
+  - `p_pkpg02_doseprop` — dose-proportionality scatter plot with power-model regression on log-log scale
+  - `l_pkpl01` / `l_pkpl01_mp` — individual PK parameter listings (all parameters and metabolite-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)
+
 ### 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)

R/export_cdisc.R

@@ -72,6 +72,8 @@ export_cdisc <- function(res_nca, grouping_vars = character(0), flag_rules = NUL
         to_match_res_cols, dose_time_col,  route_col, duration_col, conc_timeu_col,
         # Raw variables that can be directly used in PP or ADPP if present
         CDISC_COLS$PP$Variable, CDISC_COLS$ADPP$Variable,
+        # Dose amount/unit — not in ADPP CDISC metadata but needed for dose-proportionality TLGs
+        "DOSEA", "DOSEU",
         # Variables that can be used to guess other missing variables
         "PCRFTDTM", "PCRFTDTC", "PCTPTREF", "VISIT", "ATPTREF", "EXFAST",
         "PCFAST", "FEDSTATE", "EPOCH"
@@ -228,7 +230,8 @@ export_cdisc <- function(res_nca, grouping_vars = character(0), flag_rules = NUL
   adpp <- cdisc_info %>%
     select(any_of(c(
       CDISC_COLS$ADPP$Variable, "exclude", grouping_vars,
-      ".pp_excl", ".pp_excl_reason"
+      ".pp_excl", ".pp_excl_reason",
+      "DOSEA", "DOSEU"
     ))) %>%
     # Deselect permitted columns with only NAs
     select(

R/g_pkcg.R

@@ -16,6 +16,15 @@ g_pkcg01_log <- function(data, ...) {
   pkcg01(adnca = data, scale = "LOG", ...)
 }
 
+#' Wrapper around aNCA::pkcg01() function. Calls the function with `SBS` scale argument.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg01.
+#' @export
+g_pkcg01_sbs <- function(data, ...) {
+  pkcg01(adnca = data, scale = "SBS", ...)
+}
+
 #' Generate PK Concentration-Time Profile Plots
 #'
 #' This function generates a list of ggplots for PK concentration-time profiles.
@@ -359,6 +368,15 @@ g_pkcg02_log <- function(data, ...) {
   pkcg02(adnca = data, scale = "LOG", ...)
 }
 
+#' Wrapper around aNCA::pkcg02() function. Calls the function with `SBS` scale argument.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg02.
+#' @export
+g_pkcg02_sbs <- function(data, ...) {
+  pkcg02(adnca = data, scale = "SBS", ...)
+}
+
 #' Generate Combined PK Concentration-Time Profile Plot by Cohort
 #'
 #' This function generates a list of plotly objects PK concentration-time profiles by group
@@ -669,6 +687,42 @@ g_pkcg03_log <- function(data, ...) {
   pkcg03(adnca = data, scale = "LOG", ...)
 }
 
+#' Wrapper around aNCA::pkcg03() function. Calls the function with `SBS` scale argument.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg03.
+#' @export
+g_pkcg03_sbs <- function(data, ...) {
+  pkcg03(adnca = data, scale = "SBS", ...)
+}
+
+#' Wrapper around aNCA::pkcg03() function. Mean linear plot grouped by dose.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg03.
+#' @export
+p_pkcg03_lin_dose <- function(data, ...) {
+  pkcg03(adnca = data, scale = "LIN", mean_group_var = "DOSEA", ...)
+}
+
+#' Wrapper around aNCA::pkcg03() function. Mean log plot grouped by dose.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg03.
+#' @export
+p_pkcg03_log_dose <- function(data, ...) {
+  pkcg03(adnca = data, scale = "LOG", mean_group_var = "DOSEA", ...)
+}
+
+#' Wrapper around aNCA::pkcg03() function. Mean side-by-side plot grouped by dose.
+#' @param data Data to be passed into the plotting function.
+#' @param ...  Any other parameters to be passed into the plotting function.
+#' @returns ggplot2 object for pkcg03.
+#' @export
+p_pkcg03_sbs_dose <- function(data, ...) {
+  pkcg03(adnca = data, scale = "SBS", mean_group_var = "DOSEA", ...)
+}
+
 #' Generate PK Concentration-Time Profile Plots
 #'
 #' This function generates a list of ggplots for Mean PK concentration-time profiles.