From 7d1a950b1c88b409c768d24bb364994b3c9d3e17 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Tue, 15 Apr 2025 08:52:25 -0400
Subject: [PATCH] Generalize unit conversion to allow unit conversion on
 completed analyses

---
 NAMESPACE                    |  3 +++
 R/class-PKNCAdata.R          |  4 ++--
 R/unit-support.R             | 31 +++++++++++++++++++++++++++++--
 man/PKNCAdata.Rd             |  2 +-
 man/pknca_unit_conversion.Rd | 27 ++++++++++++++++++++++++++-
 5 files changed, 61 insertions(+), 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e1ee121a..248ff058 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -63,6 +63,8 @@ S3method(model.frame,PKNCAdose)
 S3method(mutate,PKNCAconc)
 S3method(mutate,PKNCAdose)
 S3method(mutate,PKNCAresults)
+S3method(pknca_unit_conversion,PKNCAresults)
+S3method(pknca_unit_conversion,data.frame)
 S3method(print,PKNCAconc)
 S3method(print,PKNCAdata)
 S3method(print,PKNCAdose)
@@ -214,6 +216,7 @@ export(pk.nca.interval)
 export(pk.tss)
 export(pk.tss.monoexponential)
 export(pk.tss.stepwise.linear)
+export(pknca_unit_conversion)
 export(pknca_units_table)
 export(right_join)
 export(roundString)
diff --git a/R/class-PKNCAdata.R b/R/class-PKNCAdata.R
index 495de041..1f19d356 100644
--- a/R/class-PKNCAdata.R
+++ b/R/class-PKNCAdata.R
@@ -54,7 +54,7 @@ PKNCAdata.PKNCAdose <- function(data.conc, data.dose, ...) {
 PKNCAdata.default <- function(data.conc, data.dose, ...,
                               formula.conc, formula.dose,
                               impute = NA_character_,
-                              intervals, units, options=list()) {
+                              intervals, units = NULL, options=list()) {
   if (length(list(...))) {
     stop("Unknown argument provided to PKNCAdata.  All arguments other than `data.conc` and `data.dose` must be named.")
   }
@@ -169,7 +169,7 @@ PKNCAdata.default <- function(data.conc, data.dose, ...,
   units_interval_end <- inherits(ret$intervals$end, "units")
 
   # Insert the unit conversion table
-  if (missing(units)) {
+  if (is.null(units)) {
     # What unit types are recognized?
     possible_units <-
       setdiff(
diff --git a/R/unit-support.R b/R/unit-support.R
index e1c97d37..318a8bc3 100644
--- a/R/unit-support.R
+++ b/R/unit-support.R
@@ -102,7 +102,15 @@ pknca_units_table <- function(concu, doseu, amountu, timeu,
       # Use the original conversions argument over `conversions_pref`
       mask_pref <- conversions_pref$PPORRESU %in% conversions$PPORRESU[idx]
       if (!any(mask_pref)) {
-        stop("Cannot find PPORRESU match between conversions and preferred unit conversions.  Check PPORRESU values in 'conversions' argument.")
+        stop(
+          paste(
+            sprintf(
+              "Cannot find PPORRESU match between conversions and preferred unit conversions (%s).",
+              paste0('"', unique(conversions_pref$PPORRESU[!mask_pref]), '"', collapse = ", ")
+            ),
+            "Check PPORRESU values in 'conversions' argument."
+          )
+        )
       }
       conversions_pref$PPSTRESU[mask_pref] <- conversions$PPSTRESU[idx]
       conversions_pref$conversion_factor[mask_pref] <- conversions$conversion_factor[idx]
@@ -391,7 +399,26 @@ pknca_units_add_paren <- function(unit) {
 #'   but not all parameters?
 #' @returns The result table with units converted
 #' @keywords Internal
-pknca_unit_conversion <- function(result, units, allow_partial_missing_units = FALSE) {
+#' @export
+pknca_unit_conversion <- function(result, units = NULL, allow_partial_missing_units = FALSE) {
+  UseMethod("pknca_unit_conversion")
+}
+
+#' @describeIn pknca_unit_conversion Convert PKNCA units for a data.frame
+#' @export
+pknca_unit_conversion.PKNCAresults <- function(result, units = NULL, allow_partial_missing_units = FALSE) {
+  result$result <-
+    pknca_unit_conversion(
+      result$result,
+      units = units,
+      allow_partial_missing_units = allow_partial_missing_units
+    )
+  result
+}
+
+#' @describeIn pknca_unit_conversion Convert PKNCA units for a data.frame
+#' @export
+pknca_unit_conversion.data.frame <- function(result, units = NULL, allow_partial_missing_units = FALSE) {
   ret <- result
   if (!is.null(units)) {
     ret <-
diff --git a/man/PKNCAdata.Rd b/man/PKNCAdata.Rd
index aac9084b..1efbccf6 100644
--- a/man/PKNCAdata.Rd
+++ b/man/PKNCAdata.Rd
@@ -21,7 +21,7 @@ PKNCAdata(data.conc, data.dose, ...)
   formula.dose,
   impute = NA_character_,
   intervals,
-  units,
+  units = NULL,
   options = list()
 )
 }
diff --git a/man/pknca_unit_conversion.Rd b/man/pknca_unit_conversion.Rd
index 1a0f9a07..1e1f5ed4 100644
--- a/man/pknca_unit_conversion.Rd
+++ b/man/pknca_unit_conversion.Rd
@@ -2,9 +2,27 @@
 % Please edit documentation in R/unit-support.R
 \name{pknca_unit_conversion}
 \alias{pknca_unit_conversion}
+\alias{pknca_unit_conversion.PKNCAresults}
+\alias{pknca_unit_conversion.data.frame}
 \title{Perform unit conversion (if possible) on PKNCA results}
 \usage{
-pknca_unit_conversion(result, units, allow_partial_missing_units = FALSE)
+pknca_unit_conversion(
+  result,
+  units = NULL,
+  allow_partial_missing_units = FALSE
+)
+
+\method{pknca_unit_conversion}{PKNCAresults}(
+  result,
+  units = NULL,
+  allow_partial_missing_units = FALSE
+)
+
+\method{pknca_unit_conversion}{data.frame}(
+  result,
+  units = NULL,
+  allow_partial_missing_units = FALSE
+)
 }
 \arguments{
 \item{result}{The results data.frame}
@@ -20,4 +38,11 @@ The result table with units converted
 \description{
 Perform unit conversion (if possible) on PKNCA results
 }
+\section{Methods (by class)}{
+\itemize{
+\item \code{pknca_unit_conversion(PKNCAresults)}: Convert PKNCA units for a data.frame
+
+\item \code{pknca_unit_conversion(data.frame)}: Convert PKNCA units for a data.frame
+
+}}
 \keyword{Internal}