Fix/parameter description 40 char limit

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(AIC,list)
 S3method(PKNCAconc,data.frame)
 S3method(PKNCAconc,default)
 S3method(PKNCAconc,tbl_df)

NEWS.md

@@ -6,6 +6,9 @@ the dosing including dose amount and route.
 
 # Development version
 
+* Parameter descriptions in `add.interval.col()` are now limited to 40
+  characters to comply with SDTM requirements.
+
 * Bug fix: `pk.nca()` no longer errors on unsorted concentration-time data.
   Group-level concentration data are now sorted by time before calculation, so
   parameters that use the full group (e.g. `aucint.all` and the other `aucint*`

R/001-add.interval.col.R

@@ -158,7 +158,7 @@ add.interval.col <- function(name,
   checkmate::assert_character(x = FUN, len = 1, any.missing = TRUE) # allows NA
   checkmate::assert_logical(x = sparse, len = 1, any.missing=FALSE)
   checkmate::assert_character(x = pretty_name, len = 1, min.chars = 1, any.missing=FALSE)
-  checkmate::assert_character(x = desc, len = 1, any.missing=FALSE)
+  checkmate::assert_character(x = desc, len = 1, any.missing=FALSE, max.chars = 40)
   checkmate::assert_character(x = depends, null.ok = TRUE)
 
   # `values` must be either a function (used to validate/coerce) or a vector
@@ -200,7 +200,7 @@ add.interval.col <- function(name,
     # Ensure formalsmap names are unique
     checkmate::assert_character(x = names(formalsmap), min.chars = 1, any.missing = FALSE)
   }
-
+  
   # Ensure that the function exists
   if (!is.na(FUN)) {
     # Ensure that the function exists
@@ -341,5 +341,5 @@ add.interval.col(
   values = as.numeric,
   unit_type="time",
   pretty_name="Interval End",
-  desc = "Ending time of the interval (potentially infinity)"
+  desc = "End time of interval (may be Inf)"
 )

R/auc.R

@@ -343,7 +343,7 @@ add.interval.col("aucinf.obs",
                  values=c(FALSE, TRUE),
                  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",
+                 desc="AUC start to inf, obs Clast extrap",
                  depends=c("lambda.z", "clast.obs"),
                  pptestcd_cdisc="AUCIFO",
                  pptest_cdisc="AUC Infinity Obs")
@@ -353,7 +353,7 @@ add.interval.col("aucinf.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",
+                 desc="AUC start to inf, pred Clast extrap",
                  depends=c("lambda.z", "clast.pred"),
                  pptestcd_cdisc="AUCIFP",
                  pptest_cdisc="AUC Infinity Pred")
@@ -363,7 +363,7 @@ add.interval.col("auclast",
                  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="AUC start to last conc above LOQ",
                  pptestcd_cdisc="AUCLST",
                  pptest_cdisc="AUC to Last Nonzero Conc")
 
@@ -372,7 +372,7 @@ add.interval.col("aucall",
                  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="AUClast plus triangle, 0 at BLQ",
                  pptestcd_cdisc="AUCALL",
                  pptest_cdisc="AUC All")
 
@@ -381,7 +381,7 @@ add.interval.col("aumcinf.obs",
                  values=c(FALSE, TRUE),
                  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",
+                 desc="AUMC start to inf, obs Clast extrap",
                  depends=c("lambda.z", "clast.obs"),
                  pptestcd_cdisc="AUMCIFO",
                  pptest_cdisc="AUMC Infinity Obs")
@@ -391,7 +391,7 @@ add.interval.col("aumcinf.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",
+                 desc="AUMC start to inf, pred Clast extrap",
                  depends=c("lambda.z", "clast.pred"),
                  pptestcd_cdisc="AUMCIFP",
                  pptest_cdisc="AUMC Infinity Pred")
@@ -401,7 +401,7 @@ add.interval.col("aumclast",
                  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="AUMC start to last conc above LOQ",
                  pptestcd_cdisc="AUMCLST",
                  pptest_cdisc="AUMC to Last Nonzero Conc")
 
@@ -410,7 +410,7 @@ add.interval.col("aumcall",
                  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="AUMClast plus triangle moment, 0 at BLQ",
                  pptestcd_cdisc="AUMCALL",
                  pptest_cdisc="AUMC All")
 

R/aucint.R

@@ -252,7 +252,7 @@ add.interval.col("aucint.last",
                  values=c(FALSE, TRUE),
                  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)",
+                 desc="AUC from T1 to T2 (zero extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  pptestcd_cdisc="AUCINT",
                  pptest_cdisc="AUC from T1 to T2")
@@ -262,7 +262,7 @@ add.interval.col("aucint.last.dose",
                  values=c(FALSE, TRUE),
                  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",
+                 desc="AUCdn T1 to T2 (zero extrap)",
                  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")
@@ -272,7 +272,7 @@ add.interval.col("aucint.all",
                  values=c(FALSE, TRUE),
                  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)",
+                 desc="AUC from T1 to T2 (AUCall extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  pptestcd_cdisc="AUCINTA",
                  pptest_cdisc="AUCint (based on AUCall extrapolation)")
@@ -282,7 +282,7 @@ add.interval.col("aucint.all.dose",
                  values=c(FALSE, TRUE),
                  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",
+                 desc="AUCdn T1 to T2 (AUCall extrap)",
                  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)")
@@ -292,7 +292,7 @@ add.interval.col("aucint.inf.obs",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  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)",
+                 desc="AUC from T1 to T2 (AUCinf,obs extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  depends=c("lambda.z", "clast.obs"),
                  pptestcd_cdisc="AUCINTIS",
@@ -303,7 +303,7 @@ add.interval.col("aucint.inf.obs.dose",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  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",
+                 desc="AUCdn T1 to T2 (AUCinf,obs extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.obs"),
                  pptestcd_cdisc="AUCINTID",
@@ -314,7 +314,7 @@ add.interval.col("aucint.inf.pred",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  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)",
+                 desc="AUC from T1 to T2 (AUCinf,pred extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  depends=c("lambda.z", "clast.pred"),
                  pptestcd_cdisc="AUCINTIP",
@@ -325,7 +325,7 @@ add.interval.col("aucint.inf.pred.dose",
                  values=c(FALSE, TRUE),
                  unit_type="auc",
                  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",
+                 desc="AUCdn T1 to T2 (AUCinf,pred extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.pred"),
                  pptestcd_cdisc="AUCINTPD",
@@ -407,7 +407,7 @@ add.interval.col("aumcint.last",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMClast extrapolation)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast)",
+                 desc="AUMC from T1 to T2 (zero extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
 
 # aumcint.last.dose (WITH dose awareness)
@@ -416,7 +416,7 @@ add.interval.col("aumcint.last.dose",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMClast extrapolation, dose-aware)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) with dose-aware interpolation/extrapolation of concentrations",
+                 desc="AUMCdn T1 to T2 (zero extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
 
 # aumcint.all (without dose awareness)
@@ -425,7 +425,7 @@ add.interval.col("aumcint.all",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCall extrapolation)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall)",
+                 desc="AUMC from T1 to T2 (AUMCall extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL))
 
 # aumcint.all.dose (WITH dose awareness)
@@ -434,7 +434,7 @@ add.interval.col("aumcint.all.dose",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCall extrapolation, dose-aware)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) with dose-aware interpolation/extrapolation of concentrations",
+                 desc="AUMCdn T1 to T2 (AUMCall extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"))
 
 # aumcint.inf.obs (without dose awareness)
@@ -443,7 +443,7 @@ add.interval.col("aumcint.inf.obs",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCinf,obs extrapolation)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast)",
+                 desc="AUMC from T1 to T2 (AUMCinf,obs extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  depends=c("lambda.z", "clast.obs"))
 
@@ -453,7 +453,7 @@ add.interval.col("aumcint.inf.obs.dose",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCinf,obs extrapolation, dose-aware)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) with dose-aware interpolation/extrapolation of concentrations",
+                 desc="AUMCdn T1 to T2 (AUMCinf,obs extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.obs"))
 
@@ -463,7 +463,7 @@ add.interval.col("aumcint.inf.pred",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCinf,pred extrapolation)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall)",
+                 desc="AUMC from T1 to T2 (AUMCinf,pred extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose=NULL),
                  depends=c("lambda.z", "clast.pred"))
 
@@ -473,7 +473,7 @@ add.interval.col("aumcint.inf.pred.dose",
                  values=c(FALSE, TRUE),
                  unit_type="aumc",
                  pretty_name="AUMCint (based on AUMCinf,pred extrapolation, dose-aware)",
-                 desc="The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) with dose-aware interpolation/extrapolation of concentrations",
+                 desc="AUMCdn T1 to T2 (AUMCinf,pred extrap)",
                  formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.pred"))