From 656466946f093617ababebe5ec3b36809234112a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 15 May 2015 08:49:40 +0200
Subject: Finished migration from RUnit to testthat

---
 tests/testthat/test_schaefer07_complex_case.R | 68 +++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 tests/testthat/test_schaefer07_complex_case.R

(limited to 'tests/testthat/test_schaefer07_complex_case.R')

diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R
new file mode 100644
index 00000000..1ef5106e
--- /dev/null
+++ b/tests/testthat/test_schaefer07_complex_case.R
@@ -0,0 +1,68 @@
+# Copyright (C) 2014-2015 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+# This test was migrated from a RUnit test inst/unitTests/runit.mkinfit.R
+
+context("Complex test case from Schaefer et al. (2007) Piacenza paper")
+
+schaefer07_complex_model <- mkinmod(
+  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+  A1 = list(type = "SFO", to = "A2"),
+  B1 = list(type = "SFO"),
+  C1 = list(type = "SFO"),
+  A2 = list(type = "SFO"), use_of_ff = "max")
+
+schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+
+fit.default <- mkinfit(schaefer07_complex_model, schaefer07_long, quiet = TRUE)
+
+test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {
+  
+  s <- summary(fit.default)
+  r <- schaefer07_complex_results
+
+  with(as.list(fit.default$bparms.optim), {
+    r$mkin <<- c(
+      k_parent,
+      s$distimes["parent", "DT50"],
+      s$ff["parent_A1"],
+      k_A1,
+      s$distimes["A1", "DT50"],
+      s$ff["parent_B1"],
+      k_B1,
+      s$distimes["B1", "DT50"],
+      s$ff["parent_C1"],
+      k_C1,
+      s$distimes["C1", "DT50"],
+      s$ff["A1_A2"],
+      k_A2,
+      s$distimes["A2", "DT50"])
+    }
+  )
+  r$means <- (r$KinGUI + r$ModelMaker)/2
+  r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
+  expect_equal(r$mkin.deviation < 10, rep(TRUE, 14))
+})
+
+test_that("We avoid the local minumum with default settings", {
+  # If we use optimisation algorithm 'Marq' we get a local minimum with a
+  # sum of squared residuals of 273.3707
+  # When using 'Marq', we need to give a good starting estimate e.g. for k_A2 in
+  # order to get the optimum with sum of squared residuals 240.5686
+  expect_equal(round(fit.default$ssr, 4), 240.5686)
+})
-- 
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