intervals argument to PKNCAdata may now be a tibble (fix #72)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PKNCA
 Type: Package
 Title: Perform Pharmacokinetic Non-Compartmental Analysis
-Version: 0.8.5.9007
+Version: 0.8.5.9008
 Authors@R: c(
     person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X")),
     person("Clare", "Buckeridge", email="clare.buckeridge@pfizer.com", role="aut"),

NEWS.md

@@ -20,6 +20,7 @@ the dosing including dose amount and route.
   `PKNCAresults` objects.
 * `PKNCAdata()` is more restrictive on unknown arguments issuing an error
   when unknonwn arguments are present.
+* `intervals` argument to `PKNCAdata()` may now be a tibble (fixes #72).
 
 # PKNCA 0.8.5
 

R/pk.calc.all.R

@@ -228,7 +228,7 @@ pk.nca.intervals <- function(conc.dose, intervals, options) {
             duration.dose.group=dose_data_group[[col.duration.dose]],
             route.group=dose_data_group[[col.route]],
             # Generic data
-            interval=all.intervals[i,],
+            interval=all.intervals[i, , drop=FALSE],
             options=options)
           if (!is.null(col.include_half.life)) {
             args$include_half.life <- conc_data_interval[[col.include_half.life]]
@@ -305,8 +305,9 @@ pk.nca.interval <- function(conc, time, volume, duration.conc,
                             dose.group=NULL, time.dose.group=NULL, duration.dose.group=NULL, route.group=NULL,
                             include_half.life=NULL, exclude_half.life=NULL,
                             interval, options=list()) {
-  if (!is.data.frame(interval))
+  if (!is.data.frame(interval)) {
     stop("interval must be a data.frame")
+  }
   if (nrow(interval) != 1)
     stop("interval must be a one-row data.frame")
   ## Prepare the return value using SDTM names
@@ -325,13 +326,16 @@ pk.nca.interval <- function(conc, time, volume, duration.conc,
   }
   ## Make sure that we calculate all of the dependencies.  Do this in
   ## reverse order for dependencies of dependencies.
-  for (n in rev(names(all.intervals)))
-    if (interval[1,n])
-      for (deps in all.intervals[[n]]$depends)
+  for (n in rev(names(all.intervals))) {
+    if (interval[[1,n]]) {
+      for (deps in all.intervals[[n]]$depends) {
         interval[1,deps] <- TRUE
+      }
+    }
+  }
   ## Do the calculations
   for (n in names(all.intervals))
-    if (interval[1,n] & !is.na(all.intervals[[n]]$FUN)) {
+    if (interval[[1,n]] & !is.na(all.intervals[[n]]$FUN)) {
       call.args <- list()
       ## Prepare to call the function by setting up its arguments.
       ## Ignore the "..." argument if it exists.

tests/testthat/test-class-PKNCAdata.R

@@ -321,4 +321,20 @@ test_that("Ensure that unexpected arguments to PKNCAdata give an error (related
     PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
   expect_error(mydata <- PKNCAdata(obj.conc, obj.dose, 1),
                regexp="Unknown argument")
-})
+})
+
+test_that("intervals may be a tibble", {
+  tmp.conc <- generate.conc(nsub=2, ntreat=1, time.points=0:24)
+  tmp.dose <- generate.dose(tmp.conc)
+  obj.conc <-
+    PKNCAconc(tmp.conc, formula=conc~time|treatment+ID)
+  obj.dose <-
+    PKNCAdose(tmp.dose, formula=dose~time|treatment+ID)
+  intervals <- data.frame(start=0, end=24, aucinf.obs=TRUE)
+  mydata_tibble <- PKNCAdata(obj.conc, obj.dose, intervals=as_data_frame(intervals))
+  mydata <- PKNCAdata(obj.conc, obj.dose, intervals=intervals)
+  expect_equal(
+    as.data.frame(pk.nca(mydata_tibble)),
+    as.data.frame(pk.nca(mydata))
+  )
+})