From 61fd1fb46d03368d213e705c333b70c4d5e8fc16 Mon Sep 17 00:00:00 2001
From: Bill Denney <billdenney@users.noreply.github.com>
Date: Mon, 21 Dec 2015 22:17:15 -0500
Subject: [PATCH] Fixes #8, when providing time to calculations within an
 interval, subtract away the time for th beginning of the interval.  For
 example, Tmax on day 14 should be between 0 and 24 not 2*7*24+c(0, 24)

---
 R/pk.calc.all.R                   |  4 +-
 tests/testthat/test-pk.calc.all.R | 72 +++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 1 deletion(-)

diff --git a/R/pk.calc.all.R b/R/pk.calc.all.R
index 4efb78da..3cc212b5 100644
--- a/R/pk.calc.all.R
+++ b/R/pk.calc.all.R
@@ -146,7 +146,9 @@ pk.nca.interval <- function(conc, time, interval, options=list()) {
         if (arg == "conc") {
           call.args[[arg]] <- conc
         } else if (arg == "time") {
-          call.args[[arg]] <- time
+          ## Realign the time to be relative to the start of the
+          ## interval
+          call.args[[arg]] <- time - interval$start[1]
         } else if (arg == "options") {
           call.args[[arg]] <- options
         } else if (any(mask.arg <- ret$PPTESTCD %in% arg)) {
diff --git a/tests/testthat/test-pk.calc.all.R b/tests/testthat/test-pk.calc.all.R
index d174439f..186a3ad7 100644
--- a/tests/testthat/test-pk.calc.all.R
+++ b/tests/testthat/test-pk.calc.all.R
@@ -1,2 +1,74 @@
 context("All NCA calculations")
 
+source("generate.data.R")
+
+test_that("pk.nca", {
+  ## Note that generate.conc sets the random seed, so it doesn't have
+  ## to happen here.
+  tmpconc <- generate.conc(2, 1, 0:24)
+  tmpdose <- generate.dose(tmpconc)
+  myconc <- PKNCAconc(tmpconc, conc~time|treatment+ID)
+  mydose <- PKNCAdose(tmpdose, dose~time|treatment+ID)
+  mydata <- PKNCAdata(myconc, mydose)
+  myresult <- pk.nca(mydata)
+
+  expect_equal(names(myresult),
+               c("result", "data", "provenance"),
+               info="Make sure that the result has the expected names (and only the expected names) in it.")
+  
+  ## Test each of the pieces for myresult for accuracy
+
+  expect_equal(myresult$data, {
+    tmp <- mydata
+    ## The options should be the default options after the
+    ## calculations are done.
+    tmp$options <- PKNCA.options()
+    tmp
+  }, info="The data is just a copy of the input data plus an instantiation of the PKNCA.options")
+
+  ## The specific order of the levels isn't important-- the fact that
+  ## they are factors and that the set doesn't change is important.
+  test.code.levels <- levels(myresult$result$PPTESTCD)
+  verify.result <-
+    data.frame(
+      start=0,
+      end=c(24, rep(Inf, 12),
+            24, rep(Inf, 12)),
+      treatment="Trt 1",
+      ID=rep(c(1, 2), each=13),
+      PPTESTCD=factor(rep(c("auclast", "cmax", "tmax", "tlast",
+                            "lambda.z", "r.squared", "adj.r.squared",
+                            "lambda.z.time.first", "lambda.z.n.points",
+                            "clast.pred", "half.life", "span.ratio",
+                            "aucinf"),
+                          times=2),
+                      levels=test.code.levels),
+      PPORRES=c(13.54, 0.9998, 4.000, 24.00,
+                0.04297, 0.9072, 0.9021, 5.000,
+                20.00, 0.3356, 16.13, 1.178,
+                21.55, 14.03, 0.9410, 2.000,
+                24.00, 0.05689, 0.9000, 0.8944,
+                5.000, 20.00, 0.3011, 12.18,
+                1.560, 19.56),
+      stringsAsFactors=FALSE)
+  expect_equal(myresult$result, verify.result,
+               tol=0.001)
+
+  ## Dosing not at time 0
+  tmpconc.multi <- generate.conc(2, 1, 0:24)
+  tmpdose.multi <- generate.dose(tmpconc)
+  tmpconc.multi$time <- tmpconc.multi$time + 2
+  tmpdose.multi$time <- tmpdose.multi$time + 2
+  myconc.multi <- PKNCAconc(tmpconc.multi, conc~time|treatment+ID)
+  mydose.multi <- PKNCAdose(tmpdose.multi, dose~time|treatment+ID)
+  mydata.multi <- PKNCAdata(myconc.multi, mydose.multi)
+  myresult.multi <- pk.nca(mydata.multi)
+
+  verify.result.multi <- verify.result
+  verify.result.multi$start <- verify.result.multi$start + 2
+  verify.result.multi$end <- verify.result.multi$end + 2
+  expect_equal(myresult.multi$result, verify.result.multi,
+               tol=0.001,
+               info="Shifted dosing works the same as un-shifted where time parameters like tmax and tlast are reported relative to the start of the interval")
+
+})