Fix tests

NAMESPACE

@@ -189,6 +189,12 @@ export(pk.calc.aumc.inf)
 export(pk.calc.aumc.inf.obs)
 export(pk.calc.aumc.inf.pred)
 export(pk.calc.aumc.last)
+export(pk.calc.aumcint)
+export(pk.calc.aumcint.all)
+export(pk.calc.aumcint.inf.obs)
+export(pk.calc.aumcint.inf.pred)
+export(pk.calc.aumcint.last)
+export(pk.calc.aumciv)
 export(pk.calc.auxc)
 export(pk.calc.c0)
 export(pk.calc.cav)
@@ -204,6 +210,9 @@ export(pk.calc.cstart)
 export(pk.calc.ctrough)
 export(pk.calc.deg.fluc)
 export(pk.calc.dn)
+export(pk.calc.ermax)
+export(pk.calc.ertlst)
+export(pk.calc.ertmax)
 export(pk.calc.f)
 export(pk.calc.fe)
 export(pk.calc.half.life)
@@ -214,6 +223,8 @@ export(pk.calc.mrt.md)
 export(pk.calc.ptr)
 export(pk.calc.sparse_auc)
 export(pk.calc.sparse_auclast)
+export(pk.calc.sparse_aumc)
+export(pk.calc.sparse_aumclast)
 export(pk.calc.swing)
 export(pk.calc.tfirst)
 export(pk.calc.thalf.eff)
@@ -244,6 +255,7 @@ export(superposition)
 export(time_calc)
 export(ungroup)
 export(var_sparse_auc)
+export(var_sparse_aumc)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)

R/PKNCA.options.R

@@ -142,6 +142,28 @@
     }
     x
   },
+  first.ertmax=function(x, default=FALSE, description=FALSE) {
+    if (description)
+      return(paste(
+        "If there is more than one concentration equal to maximum excretion rate, which time",
+        "should be selected for ertmax?  If 'TRUE', the first will be selected.",
+        "If 'FALSE', the last will be selected."))
+    if (default)
+      return(TRUE)
+    if (length(x) != 1)
+      stop("first.ertmax must be a scalar")
+    if (is.na(x))
+      stop("first.ertmax may not be NA")
+    if (!is.logical(x)) {
+      x <- as.logical(x)
+      if (is.na(x)) {
+        stop("Could not convert first.ertmax to a logical value")
+      } else {
+        warning("Converting first.ertmax to a logical value: ", x)
+      }
+    }
+    x
+  },
   first.tmax=function(x, default=FALSE, description=FALSE) {
     if (description)
       return(paste(
@@ -579,4 +601,3 @@ PKNCA.set.summary <- function(name, description, point, spread,
   assign("summary", current, envir=.PKNCAEnv)
   invisible(current)
 }
-

R/pk.calc.urine.R

@@ -240,11 +240,11 @@ PKNCA.set.summary(
 #' @param time The starting time of the collection interval
 #' @param duration.conc The duration of the collection interval
 #' @param check Should the concentration and time data be checked?
-#' @param first.tmax If TRUE, return the first time of maximum excretion rate; otherwise, return the last
+#' @param first.ertmax If TRUE, return the first time of maximum excretion rate; otherwise, return the last
 #' @return The midpoint collection time of the maximum excretion rate, or NA if not available
 #' @export
-pk.calc.ertmax <- function(conc, volume, time, duration.conc, check = TRUE, first.tmax = NULL) {
-
+pk.calc.ertmax <- function(conc, volume, time, duration.conc, check = TRUE, first.ertmax = NULL) {
+  first.ertmax <- PKNCA.choose.option(name="first.ertmax", value=first.ertmax, options=options)
   # Generate messages about missing concentrations/volumes
   message_all <- generate_missing_messages(conc, volume,
                                            name_a = "concentrations",
@@ -258,7 +258,7 @@ pk.calc.ertmax <- function(conc, volume, time, duration.conc, check = TRUE, firs
     midtime <- time + duration.conc / 2
     ret <- midtime[er %in% ermax]
 
-    if (first.tmax) {
+    if (first.ertmax) {
       ret <- ret[1]
     } else {
       ret <- ret[length(ret)]
@@ -299,32 +299,32 @@ generate_missing_messages <- function(a, b,
 
   mask_a <- is.na(a)
   mask_b <- is.na(b)
-  
+
   mask_both <- mask_a & mask_b
   mask_a_only <- mask_a & !mask_both
   mask_b_only <- mask_b & !mask_both
-  
+
   msg_both <- msg_a <- msg_b <- NA_character_
   n <- length(mask_a)
-  
+
   if (all(mask_both)) {
     msg_both <- sprintf("All %s and %s are missing", name_a, name_b)
   } else if (any(mask_both)) {
     msg_both <- sprintf("%g of %g %s and %s are missing", sum(mask_both), n, name_a, name_b)
   }
-  
+
   if (all(mask_a_only)) {
     msg_a <- sprintf("All %s are missing", name_a)
   } else if (any(mask_a_only)) {
     msg_a <- sprintf("%g of %g %s are missing", sum(mask_a_only), n, name_a)
   }
-  
+
   if (all(mask_b_only)) {
     msg_b <- sprintf("All %s are missing", name_b)
   } else if (any(mask_b_only)) {
     msg_b <- sprintf("%g of %g %s are missing", sum(mask_b_only), n, name_b)
   }
-  
+
   # Return non-NA messages
   stats::na.omit(c(msg_both, msg_a, msg_b))
 }