feat: add CDISC PPTESTCD/PPTEST columns to PKNCAresults

NEWS.md

@@ -6,6 +6,20 @@ the dosing including dose amount and route.
 
 # PKNCA 0.12.2
 
+## Features added
+
+* `add.interval.col()` gains `pptestcd_cdisc` and `pptest_cdisc` arguments for
+  CDISC standard parameter code and name mappings.  Route-dependent parameters
+  (CL, VZ, MRT, VSS) accept a nested list to distinguish intravascular and
+  extravascular CDISC codes (#403)
+* `as.data.frame.PKNCAresults()` gains `out_format = "cdisc"` to translate
+  PPTESTCD to CDISC standard codes and add a PPTEST column.  Route-dependent
+  translations are resolved from the dose data (#403)
+* When `out_format = "cdisc"` and any parameter has "INT" in its PPTESTCD,
+  PPSTINT and PPENINT columns are added with ISO 8601 durations relative to
+  the last dose time.  The time unit is taken from `timeu_pref` or `timeu`
+  (#403)
+
 ## Bug Fixes
 
 * `normalize.data.frame()` no longer triggers a dplyr deprecation warning

R/001-add.interval.col.R

@@ -23,6 +23,13 @@ assign("interval.cols", list(), envir=.PKNCAEnv)
 #'   to NCA parameter names.  See the details for information on use of
 #'   `formalsmap`.
 #' @param datatype The type of data used for the calculation
+#' @param pptestcd_cdisc The CDISC PPTESTCD code for this parameter.  Can be a
+#'   character string for simple mappings, or a named list for route-dependent
+#'   mappings (e.g., `list(route = list(extravascular = "CLF/FO", intravascular
+#'   = "CLO"))`).  Defaults to `name` if not provided.
+#' @param pptest_cdisc The CDISC PPTEST name for this parameter.  Can be a
+#'   character string or a named list (same structure as `pptestcd_cdisc`).
+#'   Defaults to `desc` if not provided.
 #' @returns NULL (Calling this function has a side effect of changing the
 #'   available intervals for calculations)
 #'
@@ -90,7 +97,9 @@ add.interval.col <- function(name,
                              formalsmap=list(),
                              datatype=c("interval",
                                "individual",
-                               "population")) {
+                               "population"),
+                             pptestcd_cdisc=NULL,
+                             pptest_cdisc=NULL) {
   # Check inputs
   if (!is.character(name)) {
     stop("name must be a character string")
@@ -159,6 +168,21 @@ add.interval.col <- function(name,
       stop("All names for the formalsmap list must be arguments to the function.")
     }
   }
+  # Default CDISC mappings to name/desc when not provided
+  if (is.null(pptestcd_cdisc)) {
+    pptestcd_cdisc <- name
+  }
+  if (is.null(pptest_cdisc)) {
+    pptest_cdisc <- desc
+  }
+  # Validate CDISC arguments: must be a character string or a named list
+  # with a "route" element containing named sub-elements
+  if (!is.character(pptestcd_cdisc) && !is.list(pptestcd_cdisc)) {
+    stop("pptestcd_cdisc must be a character string or a list")
+  }
+  if (!is.character(pptest_cdisc) && !is.list(pptest_cdisc)) {
+    stop("pptest_cdisc must be a character string or a list")
+  }
   current <- get("interval.cols", envir=.PKNCAEnv)
   current[[name]] <-
     list(
@@ -170,7 +194,9 @@ add.interval.col <- function(name,
       sparse=sparse,
       formalsmap=formalsmap,
       depends=depends,
-      datatype=datatype
+      datatype=datatype,
+      pptestcd_cdisc=pptestcd_cdisc,
+      pptest_cdisc=pptest_cdisc
     )
   assign("interval.cols", current, envir=.PKNCAEnv)
 }

R/auc.R

@@ -313,29 +313,37 @@ add.interval.col("aucinf.obs",
                  unit_type="auc",
                  pretty_name="AUCinf,obs",
                  desc="The area under the concentration time curve from the beginning of the interval to infinity with extrapolation to infinity from the observed Clast",
-                 depends=c("lambda.z", "clast.obs"))
+                 depends=c("lambda.z", "clast.obs"),
+                 pptestcd_cdisc="AUCIFO",
+                 pptest_cdisc="AUC Infinity Obs")
 
 add.interval.col("aucinf.pred",
                  FUN="pk.calc.auc.inf.pred",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  pretty_name="AUCinf,pred",
                  desc="The area under the concentration time curve from the beginning of the interval to infinity with extrapolation to infinity from the predicted Clast",
-                 depends=c("lambda.z", "clast.pred"))
+                 depends=c("lambda.z", "clast.pred"),
+                 pptestcd_cdisc="AUCIFP",
+                 pptest_cdisc="AUC Infinity Pred")
 
 add.interval.col("auclast",
                  FUN="pk.calc.auc.last",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  pretty_name="AUClast",
-                 desc="The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification")
+                 desc="The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification",
+                 pptestcd_cdisc="AUCLST",
+                 pptest_cdisc="AUC to Last Nonzero Conc")
 
 add.interval.col("aucall",
                  FUN="pk.calc.auc.all",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  pretty_name="AUCall",
-                 desc="The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification plus the triangle from that last concentration to 0 at the first concentration below the limit of quantification"
+                 desc="The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification plus the triangle from that last concentration to 0 at the first concentration below the limit of quantification",
+                 pptestcd_cdisc="AUCALL",
+                 pptest_cdisc="AUC All"
 )
 
 add.interval.col("aumcinf.obs",
@@ -344,29 +352,37 @@ add.interval.col("aumcinf.obs",
                  unit_type="aumc",
                  pretty_name="AUMC,inf,obs",
                  desc="The area under the concentration time moment curve from the beginning of the interval to infinity with extrapolation to infinity from the observed Clast",
-                 depends=c("lambda.z", "clast.obs"))
+                 depends=c("lambda.z", "clast.obs"),
+                 pptestcd_cdisc="AUMCIFO",
+                 pptest_cdisc="AUMC Infinity Obs")
 
 add.interval.col("aumcinf.pred",
                  FUN="pk.calc.aumc.inf.pred",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMC,inf,pred",
                  desc="The area under the concentration time moment curve from the beginning of the interval to infinity with extrapolation to infinity from the predicted Clast",
-                 depends=c("lambda.z", "clast.pred"))
+                 depends=c("lambda.z", "clast.pred"),
+                 pptestcd_cdisc="AUMCIFP",
+                 pptest_cdisc="AUMC Infinity Pred")
 
 add.interval.col("aumclast",
                  FUN="pk.calc.aumc.last",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMC,last",
-                 desc="The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification")
+                 desc="The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification",
+                 pptestcd_cdisc="AUMCLST",
+                 pptest_cdisc="AUMC to Last Nonzero Conc")
 
 add.interval.col("aumcall",
                  FUN="pk.calc.aumc.all",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMC,all",
-                 desc="The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification plus the moment of the triangle from that last concentration to 0 at the first concentration below the limit of quantification")
+                 desc="The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification plus the moment of the triangle from that last concentration to 0 at the first concentration below the limit of quantification",
+                 pptestcd_cdisc="AUMCALL",
+                 pptest_cdisc="AUMC All")
 
 PKNCA.set.summary(
   name=

R/aucint.R

@@ -243,7 +243,9 @@ add.interval.col("aucint.last",
                  unit_type="auc",
                  pretty_name="AUCint (based on AUClast extrapolation)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast)",
-                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
+                 pptestcd_cdisc="AUCINT",
+                 pptest_cdisc="AUC from T1 to T2")
 PKNCA.set.summary(
   name="aucint.last",
   description="geometric mean and geometric coefficient of variation",
@@ -257,7 +259,9 @@ add.interval.col("aucint.last.dose",
                  unit_type="auc",
                  pretty_name="AUCint (based on AUClast extrapolation, dose-aware)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations",
-                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
+                 pptestcd_cdisc="AUCINTD",
+                 pptest_cdisc="AUC from T1 to T2 Normalized by Dose")
 PKNCA.set.summary(
   name="aucint.last.dose",
   description="geometric mean and geometric coefficient of variation",
@@ -271,7 +275,9 @@ add.interval.col("aucint.all",
                  unit_type="auc",
                  pretty_name="AUCint (based on AUCall extrapolation)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall)",
-                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
+                 pptestcd_cdisc="AUCINTA",
+                 pptest_cdisc="AUCint (based on AUCall extrapolation)")
 PKNCA.set.summary(
   name="aucint.all",
   description="geometric mean and geometric coefficient of variation",
@@ -285,7 +291,9 @@ add.interval.col("aucint.all.dose",
                  unit_type="auc",
                  pretty_name="AUCint (based on AUCall extrapolation, dose-aware)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations",
-                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
+                 pptestcd_cdisc="AUCINTAD",
+                 pptest_cdisc="AUCint (based on AUCall extrapolation, dose-aware)")
 PKNCA.set.summary(
   name="aucint.all.dose",
   description="geometric mean and geometric coefficient of variation",
@@ -300,7 +308,9 @@ add.interval.col("aucint.inf.obs",
                  pretty_name="AUCint (based on AUCinf,obs extrapolation)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
-                 depends=c("lambda.z", "clast.obs"))
+                 depends=c("lambda.z", "clast.obs"),
+                 pptestcd_cdisc="AUCINTIS",
+                 pptest_cdisc="AUCint (based on AUCinf,obs extrapolation)")
 PKNCA.set.summary(
   name="aucint.inf.obs",
   description="geometric mean and geometric coefficient of variation",
@@ -315,7 +325,9 @@ add.interval.col("aucint.inf.obs.dose",
                  pretty_name="AUCint (based on AUCinf,obs extrapolation, dose-aware)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
-                 depends=c("lambda.z", "clast.obs"))
+                 depends=c("lambda.z", "clast.obs"),
+                 pptestcd_cdisc="AUCINTID",
+                 pptest_cdisc="AUCint (based on AUCinf,obs extrapolation, dose-aware)")
 PKNCA.set.summary(
   name="aucint.inf.obs.dose",
   description="geometric mean and geometric coefficient of variation",
@@ -330,7 +342,9 @@ add.interval.col("aucint.inf.pred",
                  pretty_name="AUCint (based on AUCinf,pred extrapolation)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
-                 depends=c("lambda.z", "clast.pred"))
+                 depends=c("lambda.z", "clast.pred"),
+                 pptestcd_cdisc="AUCINTIP",
+                 pptest_cdisc="AUCint (based on AUCinf,pred extrapolation)")
 PKNCA.set.summary(
   name="aucint.inf.pred",
   description="geometric mean and geometric coefficient of variation",
@@ -345,7 +359,9 @@ add.interval.col("aucint.inf.pred.dose",
                  pretty_name="AUCint (based on AUCinf,pred extrapolation, dose-aware)",
                  desc="The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
-                 depends=c("lambda.z", "clast.pred"))
+                 depends=c("lambda.z", "clast.pred"),
+                 pptestcd_cdisc="AUCINTPD",
+                 pptest_cdisc="AUCint (based on AUCinf,pred extrapolation, dose-aware)")
 PKNCA.set.summary(
   name="aucint.inf.pred.dose",
   description="geometric mean and geometric coefficient of variation",

R/auciv.R

@@ -52,7 +52,9 @@ add.interval.col(
   depends = c("auclast", "c0"),
   desc = "The AUClast calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="auclast")
+  formalsmap = list(auc="auclast"),
+  pptestcd_cdisc="AUCIVLST",
+  pptest_cdisc="AUClast (IV dosing)"
 )
 
 add.interval.col(
@@ -63,7 +65,9 @@ add.interval.col(
   depends = c("aucall", "c0"),
   desc = "The AUCall calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="aucall")
+  formalsmap = list(auc="aucall"),
+  pptestcd_cdisc="AUCIVA",
+  pptest_cdisc="AUCall (IV dosing)"
 )
 
 add.interval.col(
@@ -74,7 +78,9 @@ add.interval.col(
   depends = c("aucint.last", "c0"),
   desc = "The AUCint,last calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="aucint.last")
+  formalsmap = list(auc="aucint.last"),
+  pptestcd_cdisc="AUCIVILT",
+  pptest_cdisc="AUCint,last (IV dosing)"
 )
 
 add.interval.col(
@@ -85,7 +91,9 @@ add.interval.col(
   depends = c("aucint.all", "c0"),
   desc = "The AUCint,all calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="aucint.all")
+  formalsmap = list(auc="aucint.all"),
+  pptestcd_cdisc="AUCIVINA",
+  pptest_cdisc="AUCint,all (IV dosing)"
 )
 
 add.interval.col(
@@ -96,7 +104,9 @@ add.interval.col(
   depends = c("aucinf.obs", "c0"),
   desc = "The AUCinf,obs calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="aucinf.obs")
+  formalsmap = list(auc="aucinf.obs"),
+  pptestcd_cdisc="AUCIVIS",
+  pptest_cdisc="AUCinf,obs (IV dosing)"
 )
 
 add.interval.col(
@@ -107,7 +117,9 @@ add.interval.col(
   depends = c("aucinf.pred", "c0"),
   desc = "The AUCinf,pred calculated with back-extrapolation for intravenous dosing using extrapolated C0",
   sparse = FALSE,
-  formalsmap = list(auc="aucinf.pred")
+  formalsmap = list(auc="aucinf.pred"),
+  pptestcd_cdisc="AUCIVIP",
+  pptest_cdisc="AUCinf,pred (IV dosing)"
 )
 
 PKNCA.set.summary(
@@ -135,7 +147,9 @@ add.interval.col(
   depends = c("auclast", "aucivlast"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUClast",
   sparse = FALSE,
-  formalsmap = list(auc="auclast", auciv="aucivlast")
+  formalsmap = list(auc="auclast", auciv="aucivlast"),
+  pptestcd_cdisc="AUCIVPLT",
+  pptest_cdisc="AUCbext (based on AUClast)"
 )
 
 add.interval.col(
@@ -146,7 +160,9 @@ add.interval.col(
   depends = c("aucall", "aucivall"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUCall",
   sparse = FALSE,
-  formalsmap = list(auc="aucall", auciv="aucivall")
+  formalsmap = list(auc="aucall", auciv="aucivall"),
+  pptestcd_cdisc="AUCIVPEA",
+  pptest_cdisc="AUCbext (based on AUCall)"
 )
 
 add.interval.col(
@@ -157,7 +173,9 @@ add.interval.col(
   depends = c("aucint.last", "aucivint.last"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUCint,last",
   sparse = FALSE,
-  formalsmap = list(auc="aucint.last", auciv="aucivint.last")
+  formalsmap = list(auc="aucint.last", auciv="aucivint.last"),
+  pptestcd_cdisc="AUCIVPIL",
+  pptest_cdisc="AUCbext (based on AUCint,last)"
 )
 
 add.interval.col(
@@ -168,7 +186,9 @@ add.interval.col(
   depends = c("aucint.all", "aucivint.all"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUCint,all",
   sparse = FALSE,
-  formalsmap = list(auc="aucint.all", auciv="aucivint.all")
+  formalsmap = list(auc="aucint.all", auciv="aucivint.all"),
+  pptestcd_cdisc="AUCIVPIA",
+  pptest_cdisc="AUCbext (based on AUCint,all)"
 )
 
 add.interval.col(
@@ -179,7 +199,9 @@ add.interval.col(
   depends = c("aucinf.obs", "aucivinf.obs"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUCinf,obs",
   sparse = FALSE,
-  formalsmap = list(auc="aucinf.obs", auciv="aucivinf.obs")
+  formalsmap = list(auc="aucinf.obs", auciv="aucivinf.obs"),
+  pptestcd_cdisc="AUCIVPEI",
+  pptest_cdisc="AUCbext (based on AUCinf,obs)"
 )
 
 add.interval.col(
@@ -190,7 +212,9 @@ add.interval.col(
   depends = c("aucinf.pred", "aucivinf.pred"),
   desc = "The back-extrapolation percent for intravenous dosing based on AUCinf,pred",
   sparse = FALSE,
-  formalsmap = list(auc="aucinf.pred", auciv="aucivinf.pred")
+  formalsmap = list(auc="aucinf.pred", auciv="aucivinf.pred"),
+  pptestcd_cdisc="AUCIVPEP",
+  pptest_cdisc="AUCbext (based on AUCinf,pred)"
 )
 
 PKNCA.set.summary(