diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2015-05-15 13:55:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-05-15 13:55:19 +0200 |
| commit | 6c65cba39dbca98caf3f8e69552b3454ec1721fc (patch) | |
| tree | 00252649aeccfdd13e723054c22203006cab10c6 /tests/testthat/test_schaefer07_complex_case.R | |
| parent | a26b44d15c11ebb41083fc2efab0cc91a027b55b (diff) | |
| parent | 89cd81cf47c9f05831e854d5185b5cc599745db4 (diff) | |
Merge branch 'master' into compile_odes
Conflicts
(resolved manually, deleting code that I had
integrated into the RUnit tests for testing the
compiled version):
.gitignore
DESCRIPTION
inst/unitTests/runit.mkinerrmin.R
inst/unitTests/runit.mkinfit.R
tests/testthat/test_mkinpredict_SFO_SFO.R
vignettes/FOCUS_L.html
Diffstat (limited to 'tests/testthat/test_schaefer07_complex_case.R')
| -rw-r--r-- | tests/testthat/test_schaefer07_complex_case.R | 68 |
1 files changed, 68 insertions, 0 deletions
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)
+})
|