Improve test coverage

billdenney · Jan 2, 2018 · 86a61f1 · 86a61f1
1 parent fe6e2d8
commit 86a61f1
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Showing 10 changed files with 368 additions and 209 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PKNCA
 Type: Package
 Title: Perform Pharmacokinetic Non-Compartmental Analysis
-Version: 0.8.3.9001
+Version: 0.8.3.9002
 Date: 2018-01-01
 Authors@R: c(
     person("Bill", "Denney", email="[email protected]", role=c("aut", "cre")),

diff --git a/R/aucint.R b/R/aucint.R
@@ -131,7 +131,7 @@ pk.calc.aucint <- function(conc, time, interval, start, end,
   # AUCinf traces an AUClast curve (because the interval doesn't go to
   # infinity) while AUCall and AUClast trace their own curves.
   auc.type_map <-
-    list(AUCinf="AUClast",
+    list(AUClast="AUClast",
          AUCall="AUCall",
          AUCinf="AUClast")[[auc.type]]
   pk.calc.auc(conc=conc_interp, time=time_interp,
@@ -147,31 +147,37 @@ pk.calc.aucint <- function(conc, time, interval, start, end,
 #' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations
 #'   for AUClast
 #' @export
-pk.calc.aucint.last <- function(conc, time, start, end, ..., options=list()) {
-  pk.calc.aucint(conc=conc, time=time, interval=c(start, end), options=options, ...,
+pk.calc.aucint.last <- function(conc, time, start, end, time.dose, ..., options=list()) {
+  pk.calc.aucint(conc=conc, time=time, interval=c(start, end), options=options,
+                 time.dose=time.dose,
+                 ...,
                  auc.type="AUClast")
 }
 #' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations
 #'   for AUCall
 #' @export
-pk.calc.aucint.all <- function(conc, time, start, end, ..., options=list()) {
-  pk.calc.aucint(conc=conc, time=time, interval=c(start, end), options=options, ...,
+pk.calc.aucint.all <- function(conc, time, start, end, time.dose, ..., options=list()) {
+  pk.calc.aucint(conc=conc, time=time, interval=c(start, end), options=options,
+                 time.dose=time.dose,
+                 ...,
                  auc.type="AUCall")
 }
 #' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations
 #'   for AUCinf.obs
 #' @export
-pk.calc.aucint.inf.obs <- function(conc, time, start, end, lambda.z, clast.obs, ..., options=list()) {
+pk.calc.aucint.inf.obs <- function(conc, time, start, end, time.dose, lambda.z, clast.obs, ..., options=list()) {
   pk.calc.aucint(conc=conc, time=time, interval=c(start, end),
+                 time.dose=time.dose,
                  lambda.z=lambda.z, clast=clast.obs,
                  options=options, ...,
                  auc.type="AUCinf")
 }
 #' @describeIn pk.calc.aucint Interpolate or extrapolate concentrations
 #'   for AUCinf.pred
 #' @export
-pk.calc.aucint.inf.pred <- function(conc, time, start, end, lambda.z, clast.pred, ..., options=list()) {
+pk.calc.aucint.inf.pred <- function(conc, time, start, end, time.dose, lambda.z, clast.pred, ..., options=list()) {
   pk.calc.aucint(conc=conc, time=time, interval=c(start, end),
+                 time.dose=time.dose,
                  lambda.z=lambda.z, clast=clast.pred,
                  options=options, ...,
                  auc.type="AUCinf")
@@ -181,30 +187,30 @@ add.interval.col("aucint.last",
                  FUN="pk.calc.aucint.last",
                  values=c(FALSE, TRUE),
                  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"),
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c())
 PKNCA.set.summary("aucint.last", business.geomean, business.geocv)
 
 add.interval.col("aucint.all",
                  FUN="pk.calc.aucint.all",
                  values=c(FALSE, TRUE),
                  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"),
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c())
 PKNCA.set.summary("aucint.all", business.geomean, business.geocv)
 
 add.interval.col("aucint.inf.obs",
                  FUN="pk.calc.aucint.inf.obs",
                  values=c(FALSE, TRUE),
                  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"),
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.obs"))
 PKNCA.set.summary("aucint.last", business.geomean, business.geocv)
 
 add.interval.col("aucint.inf.pred",
                  FUN="pk.calc.aucint.inf.pred",
                  values=c(FALSE, TRUE),
                  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"),
+                 formalsmap=list(conc="conc.group", time="time.group", time.dose="time.dose.group"),
                  depends=c("lambda.z", "clast.pred"))
 PKNCA.set.summary("aucint.all", business.geomean, business.geocv)
diff --git a/R/class-PKNCAconc.R b/R/class-PKNCAconc.R
@@ -53,6 +53,10 @@ PKNCAconc.tbl_df <- function(data, ...)
 PKNCAconc.data.frame <- function(data, formula, subject,
                                  time.nominal, exclude, duration, volume,
                                  exclude_half.life, include_half.life, ...) {
+  ## The data must have... data
+  if (nrow(data) == 0) {
+    stop("data must have at least one row.")
+  }
   ## Verify that all the variables in the formula are columns in the
   ## data.
   if (!all(all.vars(formula) %in% names(data))) {

diff --git a/R/class-PKNCAdose.R b/R/class-PKNCAdose.R
@@ -61,6 +61,10 @@ PKNCAdose.tbl_df <- function(data, ...)
 #' @export
 PKNCAdose.data.frame <- function(data, formula, route, rate, duration,
                                  time.nominal, exclude, ...) {
+  ## The data must have... data
+  if (nrow(data) == 0) {
+    stop("data must have at least one row.")
+  }
   ## Check inputs
   if (!missing(time.nominal)) {
     if (!(time.nominal %in% names(data))) {