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

19 files changed, 556 insertions, 431 deletions

diff --git a/.gitignore b/.gitignore
index 956fa374..d76ec9eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,6 @@ vignettes/.build.timestamp
 vignettes/mkin.tex
 vignettes/FOCUS_Z.tex
 vignettes/*cache/
+=======
+vignettes/compiled_models_cache
 mkin.Rcheck
diff --git a/DESCRIPTION b/DESCRIPTION
index e823ba5f..60ee0b84 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
 Version: 0.9-36
-Date: 2015-04-17
+Date: 2015-05-15
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
@@ -12,14 +12,14 @@ Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
 Description: Calculation routines based on the FOCUS Kinetics Report (2006).
   Includes a function for conveniently defining differential equation models,
   model solution based on eigenvalues if possible or using numerical solvers
-  and a choice of the optimisation methods made available by the FME package.
+  and a choice of the optimisation methods made available by the 'FME' package.
   If the ccSolve package and a C compiler is available, differential equation
   models are solved as compiled C functions.
   Please note that no warranty is implied for correctness of results or fitness
   for a particular purpose.
 Depends: minpack.lm, rootSolve
 Imports: FME, deSolve
-Suggests: knitr, RUnit, ccSolve, microbenchmark
+Suggests: knitr, testthat, ccSolve, microbenchmark
 License: GPL
 LazyLoad: yes
 LazyData: yes
diff --git a/GNUmakefile b/GNUmakefile
index a84c9e8e..3fe25aad 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -18,13 +18,13 @@ SDDIR ?= $(RFSVN)/www/mkin_static
 pkgfiles = NEWS \
 	   data/* \
 	   DESCRIPTION \
-	   inst/unitTests* \
 	   inst/staticdocs/README \
 	   man/* \
 	   NAMESPACE \
 	   R/* \
 	   README.md \
 	   tests/* \
+	   tests/testthat* \
 	   TODO \
 	   vignettes/*
 
@@ -69,7 +69,7 @@ clean:
 
 test: install-no-vignettes
 	cd tests;\
-		"$(RBIN)/Rscript" doRUnit.R
+		"$(RBIN)/Rscript" testthat.R
 
 vignettes/mkin.pdf: vignettes/mkin.Rnw
 	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/mkin.Rnw', dir = 'vignettes')"
@@ -105,7 +105,8 @@ winbuilder: build
 	curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/
 
 submit:
-	@echo "\nHow about make test, make check, make winbuilder and make r-forge?"
+	@echo "\nHow about make test, make check, make winbuilder"
 	@echo "\nIs the DESCRIPTION file up to date?"
+	@echo "\nIs the NEWS.md file up to date?"
 	@echo "\nAre you sure you want to release to CRAN?"
-	@echo "\nThen use the form at http://cran.r-project.org/submit.html"
+	@echo "\nThen make r-forge, commit leftover changes if any, tag the release and use the form at http://cran.r-project.org/submit.html"
diff --git a/NEWS.md b/NEWS.md
index 023f3645..de3b0400 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,10 @@
 
 # CHANGES in mkin VERSION 0.9-35
 
+## MAJOR CHANGES
+
+- Switch from RUnit to testthat for testing
+
 ## BUG FIXES
 
 - `mkinparplot()`: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit
@@ -23,6 +27,9 @@
 ## NEW FEATURES
 
 - `mkinfit()`: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.
+- A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.
+- Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA
+- Add tests based on these datasets
 
 # CHANGES in mkin VERSION 0.9-34
 
diff --git a/data/synthetic_data_for_UBA_2014.RData b/data/synthetic_data_for_UBA_2014.RData
new file mode 100644
index 00000000..12132c97
--- /dev/null
+++ b/data/synthetic_data_for_UBA_2014.RData
diff --git a/inst/unitTests/Makefile b/inst/unitTests/Makefile
deleted file mode 100644
index 8d132253..00000000
--- a/inst/unitTests/Makefile
+++ /dev/null
@@ -1,15 +0,0 @@
-TOP=../..
-PKG=${shell cd ${TOP};pwd}
-SUITE=doRUnit.R
-R=R
-
-all: inst test
-
-inst: # Install package
-	cd ${TOP}/..;\
-	${R} CMD INSTALL ${PKG}
-
-test: # Run unit tests
-	export RCMDCHECK=FALSE;\
-	cd ${TOP}/tests;\
-	${R} --vanilla --slave < ${SUITE}
diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R
deleted file mode 100644
index f4cceda6..00000000
--- a/inst/unitTests/runit.mkinerrmin.R
+++ /dev/null
@@ -1,79 +0,0 @@
-# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{
-# and check chi2 error values against values obtained with mkin 0.33
-test.FOCUS_2006_D_SFO_SFO <- function()
-{
-  SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"),
-         m1 = list(type = "SFO"), use_of_ff = "min")
-  SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),
-         m1 = list(type = "SFO"), use_of_ff = "max")
-
-  # Check fitting with default solution method, and the different possibilities
-  fit.1 <- mkinfit(SFO_SFO.1, FOCUS_2006_D)
-  fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D, solution_type = "eigen")
-  fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
-  fit.1.dc <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
-  fit.2 <- mkinfit(SFO_SFO.2, FOCUS_2006_D)
-  fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D, solution_type = "eigen")
-  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
-  fit.2.dc <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
-
-  FOCUS_2006_D_results_schaefer07_means <- c(
-    parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34)
-
-  r.1 <- c(fit.1$bparms.optim[[1]], endpoints(fit.1)$distimes[[1]])
-  r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]])
-  r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]])
-  r.1.dc <- c(fit.1.dc$bparms.optim[[1]], endpoints(fit.1.dc)$distimes[[1]])
-  r.2 <- c(fit.2$bparms.optim[[1]], endpoints(fit.2)$distimes[[1]])
-  r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]])
-  r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]])
-  r.2.dc <- c(fit.2.dc$bparms.optim[[1]], endpoints(fit.2.dc)$distimes[[1]])
-
-  dev.1 <- 100 * (r.1 - FOCUS_2006_D_results_schaefer07_means)/r.1
-  checkIdentical(as.numeric(abs(dev.1)) < 1, rep(TRUE, 3))
-  dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e 
-  checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3))
-  dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d 
-  checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3))
-  dev.1.dc <- 100 * (r.1.dc - FOCUS_2006_D_results_schaefer07_means)/r.1.dc 
-  checkIdentical(as.numeric(abs(dev.1.dc)) < 1, rep(TRUE, 3))
-  dev.2 <- 100 * (r.2 - FOCUS_2006_D_results_schaefer07_means)/r.2 
-  checkIdentical(as.numeric(abs(dev.2)) < 1, rep(TRUE, 3))
-  dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e 
-  checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3))
-  dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d 
-  checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3))
-  dev.2.dc <- 100 * (r.2.dc - FOCUS_2006_D_results_schaefer07_means)/r.2.dc 
-  checkIdentical(as.numeric(abs(dev.2.dc)) < 1, rep(TRUE, 3))
-
-  round(mkinerrmin(fit.2.e), 4)
-  round(mkinerrmin(fit.2.d), 4)
-
-  errmin.FOCUS_2006_D_rounded = data.frame(
-    err.min = c(0.0640, 0.0646, 0.0469),
-    n.optim = c(4, 2, 2),
-    df = c(15, 7, 8), 
-    row.names = c("All data", "parent", "m1"))
-  checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4),
-                     errmin.FOCUS_2006_D_rounded)
-} # }}}
-
-# Test SFO_SFO model with FOCUS_2006_E against values obtained with mkin 0.33 {{{
-test.FOCUS_2006_E_SFO_SFO <- function()
-{
-  SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),
-         m1 = list(type = "SFO"), use_of_ff = "max")
-
-  fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_E)
-
-  round(mkinerrmin(fit.2.e), 4)
-  errmin.FOCUS_2006_E_rounded = data.frame(
-    err.min = c(0.1544, 0.1659, 0.1095),
-    n.optim = c(4, 2, 2),
-    df = c(13, 7, 6),
-    row.names = c("All data", "parent", "m1"))
-  checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4),
-                     errmin.FOCUS_2006_E_rounded)
-} # }}}
-
-
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
deleted file mode 100644
index 01cbaf00..00000000
--- a/inst/unitTests/runit.mkinfit.R
+++ /dev/null
@@ -1,239 +0,0 @@
-# Copyright (C) 2010-2015 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/>

-

-# Test SFO model to a relative tolerance of 1% # {{{

-test.FOCUS_2006_SFO <- function()

-{

-  SFO.1 <- mkinmod(parent = list(type = "SFO"))

-  SFO.2 <- mkinmod(parent = list(type = "SFO"), use_of_ff = "max")

-

-  fit.A.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_A, quiet=TRUE)

-  fit.A.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_A, quiet=TRUE)

-

-  median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "A", 

-                   c(M0, k, DT50, DT90)), "median"))

-

-  fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$bparms.optim, endpoints(fit.A.SFO.1)$distimes))

-  dev.A.SFO.1 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.1.r)/median.A.SFO), digits=1))

-  checkIdentical(dev.A.SFO.1 < 1, rep(TRUE, length(dev.A.SFO.1)))

-

-  fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$bparms.optim, endpoints(fit.A.SFO.2)$distimes))

-  dev.A.SFO.2 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.2.r)/median.A.SFO), digits=1))

-  checkIdentical(dev.A.SFO.2 < 1, rep(TRUE, length(dev.A.SFO.2)))

-

-  fit.C.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_C, quiet=TRUE)

-  fit.C.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_C, quiet=TRUE)

-

-  median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "C", 

-                   c(M0, k, DT50, DT90)), "median"))

-

-  fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$bparms.optim, endpoints(fit.C.SFO.1)$distimes))

-  dev.C.SFO.1 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.1.r)/median.C.SFO), digits=1))

-  checkIdentical(dev.C.SFO.1 < 1, rep(TRUE, length(dev.C.SFO.1)))

-

-  fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$bparms.optim, endpoints(fit.C.SFO.2)$distimes))

-  dev.C.SFO.2 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.2.r)/median.C.SFO), digits=1))

-  checkIdentical(dev.C.SFO.2 < 1, rep(TRUE, length(dev.C.SFO.2)))

-} # }}}

-

-# Test FOMC model to a relative tolerance of 1% {{{

-# See kinfit vignette for a discussion of FOMC fits to FOCUS_2006_A

-# In this case, only M0, DT50 and DT90 are checked

-test.FOCUS_2006_FOMC <- function()

-{

-  FOMC <- mkinmod(parent = list(type = "FOMC"))

-

-  # FOCUS_2006_A (compare kinfit vignette for discussion) 

-  fit.A.FOMC <- mkinfit(FOMC, FOCUS_2006_A, quiet=TRUE)

-

-  median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A", 

-                   c(M0, alpha, beta, DT50, DT90)), "median"))

-

-  fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$bparms.optim, endpoints(fit.A.FOMC)$distimes[c("DT50", "DT90")]))

-  dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1))

-  dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)]

-  checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC)))

-

-  # FOCUS_2006_B

-  fit.B.FOMC <- mkinfit(FOMC, FOCUS_2006_B, quiet=TRUE)

-

-  median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B", 

-                   c(M0, alpha, beta, DT50, DT90)), "median"))

-

-  fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$bparms.optim, endpoints(fit.B.FOMC)$distimes[c("DT50", "DT90")]))

-  dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1))

-  dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)]

-  checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC)))

-

-  # FOCUS_2006_C

-  fit.C.FOMC <- mkinfit(FOMC, FOCUS_2006_C, quiet=TRUE)

-

-  median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C", 

-                   c(M0, alpha, beta, DT50, DT90)), "median"))

-

-  fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$bparms.optim, endpoints(fit.C.FOMC)$distimes[c("DT50", "DT90")]))

-  dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1))

-  dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)]

-  checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC)))

-} # }}}

-

-# Test DFOP model, tolerance of 1% with the exception of f parameter for A {{{

-test.FOCUS_2006_DFOP <- function()

-{

-  DFOP <- mkinmod(parent = list(type = "DFOP"))

-

-  # FOCUS_2006_A

-  # Results were too much dependent on algorithm, as this dataset

-  # is pretty much SFO. "Port" gave a lower deviance, but deviated from the

-  # median of FOCUS_2006 solutions

-

-  # FOCUS_2006_B

-  fit.B.DFOP <- mkinfit(DFOP, FOCUS_2006_B, quiet=TRUE)

-

-  median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", 

-                   c(M0, k1, k2, f, DT50, DT90)), "median"))

-

-  fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$bparms.optim, endpoints(fit.B.DFOP)$distimes[c("DT50", "DT90")]))

-  dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1))

-  # about 0.6% deviation for parameter f, the others are <= 0.1%

-  checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP)))

-

-  # Check the compiled version of possible FOCUS_2006_B

-  if (require(ccSolve)) {

-    checkTrue(!is.null(DFOP$compiled))

-    fit.B.DFOP.compiled <- mkinfit(DFOP, FOCUS_2006_B, solution_type = "deSolve", use_compiled = TRUE, quiet=TRUE)

-

-    fit.B.DFOP.compiled.r <- as.numeric(c(fit.B.DFOP.compiled$bparms.optim, 

-                                          endpoints(fit.B.DFOP)$distimes[c("DT50", "DT90")]))

-    dev.B.DFOP.compiled <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.compiled.r)/median.B.DFOP), digits=1))

-    # about 0.6% deviation for parameter f, the others are <= 0.1%

-    checkIdentical(dev.B.DFOP.compiled < 1, rep(TRUE, length(dev.B.DFOP)))

-  }

-} # }}}

-

-# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{

-# as they are unreliable

-test.FOCUS_2006_HS <- function()

-{

-  HS <- mkinmod(parent = list(type = "HS"))

-

-  # FOCUS_2006_A

-  fit.A.HS <- mkinfit(HS, FOCUS_2006_A, quiet=TRUE)

-

-  median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A", 

-                   c(M0, k1, k2, tb, DT50, DT90)), "median"))

-

-  fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes[c("DT50", "DT90")]))

-  dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1))

-  # about 6.7% deviation for parameter f, the others are < 0.1%

-  checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS)))

-

-  # FOCUS_2006_B

-  fit.B.HS <- mkinfit(HS, FOCUS_2006_B, quiet=TRUE)

-

-  median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B", 

-                   c(M0, k1, k2, tb, DT50, DT90)), "median"))

-

-  fit.B.HS.r <- as.numeric(c(fit.B.HS$bparms.optim, endpoints(fit.B.HS)$distimes[c("DT50", "DT90")]))

-  dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1))

-  # < 10% deviation for M0, k1, DT50 and DT90, others are problematic

-  dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)]

-  checkIdentical(dev.B.HS < 10, rep(TRUE, length(dev.B.HS)))

-

-  # FOCUS_2006_C

-  fit.C.HS <- mkinfit(HS, FOCUS_2006_C, quiet=TRUE)

-

-  median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C", 

-                   c(M0, k1, k2, tb, DT50, DT90)), "median"))

-

-  fit.C.HS.r <- as.numeric(c(fit.C.HS$bparms.optim, endpoints(fit.C.HS)$distimes[c("DT50", "DT90")]))

-  dev.C.HS <- abs(round(100 * ((median.C.HS - fit.C.HS.r)/median.C.HS), digits=1))

-  # deviation <= 0.1%

-  checkIdentical(dev.C.HS < 1, rep(TRUE, length(dev.C.HS)))

-} # }}}

-

-# Test SFORB model against DFOP solutions to a relative tolerance of 1% # {{{

-test.FOCUS_2006_SFORB <- function()

-{

-  SFORB <- mkinmod(parent = list(type = "SFORB"))

-

-  # FOCUS_2006_A

-  # Again it does not make a lot of sense to use a SFO dataset for this

-

-  # FOCUS_2006_B

-  fit.B.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE)

-  fit.B.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_B, solution_type = "deSolve", quiet=TRUE)

-

-  median.B.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", 

-                   c(M0, k1, k2, DT50, DT90)), "median"))

-

-  fit.B.SFORB.1.r <- as.numeric(c(

-                      parent_0 = fit.B.SFORB.1$bparms.optim[[1]], 

-                      k1 = endpoints(fit.B.SFORB.1)$SFORB[[1]],

-                      k2 = endpoints(fit.B.SFORB.1)$SFORB[[2]],

-                      endpoints(fit.B.SFORB.1)$distimes[c("DT50", "DT90")]))

-  dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1))

-  checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1)))

-

-  fit.B.SFORB.2.r <- as.numeric(c(

-                      parent_0 = fit.B.SFORB.2$bparms.optim[[1]], 

-                      k1 = endpoints(fit.B.SFORB.2)$SFORB[[1]],

-                      k2 = endpoints(fit.B.SFORB.2)$SFORB[[2]],

-                      endpoints(fit.B.SFORB.2)$distimes[c("DT50", "DT90")]))

-  dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1))

-  checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2)))

-} # }}}

-

-# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{

-test.mkinfit.schaefer07_complex_example <- function()

-{

-  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")

-  

-  # If we use the default algorithm 'Marq' we need to give a good starting 

-  # estimate for k_A2 in order to find the solution published by Schaefer et al.

-  fit <- mkinfit(schaefer07_complex_model, method.modFit = "Port",

-    mkin_wide_to_long(schaefer07_complex_case, time = "time"))

-  s <- summary(fit)

-  r <- schaefer07_complex_results

-  attach(as.list(fit$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))

-  checkIdentical(r$mkin.deviation < 10, rep(TRUE, 14))

-} # }}}

-

-# vim: set foldmethod=marker ts=2 sw=2 expandtab:

diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd
new file mode 100644
index 00000000..5d924afd
--- /dev/null
+++ b/man/synthetic_data_for_UBA.Rd
@@ -0,0 +1,65 @@
+\name{synthetic_data_for_UBA_2014}

+\alias{synthetic_data_for_UBA_2014}

+\docType{data}

+\title{

+  Synthetic datasets for one parent compound with two metabolites

+}

+\description{

+ The 12 datasets were generated using four different models and three different

+ variance components. The four models are either the SFO or the DFOP model with either

+ two sequential or two parallel metabolites.

+

+ Variance component 'a' is based on a normal distribution with standard deviation of 3,

+ Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.

+ Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the 

+ minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07

+ for the increase of the standard deviation with y.

+

+ Initial concentrations for metabolites and all values where adding the variance component resulted

+ in a value below the assumed limit of detection of 0.1 were set to \code{NA}.

+

+ As an example, the first dataset has the title \code{SFO_lin_a} and is based on the SFO model

+ with two sequential metabolites (linear pathway), with added variance component 'a'.

+

+ Compare also the code in the example section to see the degradation models.

+}

+\usage{synthetic_data_for_UBA_2014}

+\format{

+  A list containing datasets in the form internally used by the 'gmkin' package.

+  The list has twelfe components. Each of the components is one dataset that has,

+  among others, the following components

+  \describe{

+    \item{\code{title}}{The name of the dataset, e.g. \code{SFO_lin_a}}

+    \item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}}

+  }

+}

+\source{

+  Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative

+  zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452

+ 

+  Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for

+  measurement error in analytical chemistry. Technometrics 37(2), 176-184.

+}

+\examples{

+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),

+                           M1 = list(type = "SFO", to = "M2"),

+                           M2 = list(type = "SFO"), use_of_ff = "max")

+

+

+m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),

+                                         sink = FALSE),

+                           M1 = list(type = "SFO"),

+                           M2 = list(type = "SFO"), use_of_ff = "max")

+

+m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),

+                            M1 = list(type = "SFO", to = "M2"),

+                            M2 = list(type = "SFO"), use_of_ff = "max")

+

+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),

+                                          sink = FALSE),

+                            M1 = list(type = "SFO"),

+                            M2 = list(type = "SFO"), use_of_ff = "max")

+

+mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)

+}

+\keyword{datasets}

diff --git a/tests/doRUnit.R b/tests/doRUnit.R
deleted file mode 100644
index 9faee940..00000000
--- a/tests/doRUnit.R
+++ /dev/null
@@ -1,42 +0,0 @@
-# Adapted from a version around 2.9 of the rcdk package by Rajarshi Guha
-if(require("RUnit", quietly=TRUE)) {
- 
-  pkg <- "mkin"
-  path <- system.file(package=pkg, "unitTests")
-
-  cat("\nRunning unit tests\n")
-  print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
- 
-  library(package=pkg, character.only=TRUE)
- 
-  ## Define tests
-  testSuite <- defineTestSuite(name=paste(pkg, " Unit Tests"),
-                                          dirs=path)
-  ## Run
-  tests <- runTestSuite(testSuite)
- 
-  ## Default report name
-  pathReport <- file.path(path, "report")
- 
-  ## Report to stdout and text files
-  cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
-  printTextProtocol(tests, showDetails=FALSE)
-  printTextProtocol(tests, showDetails=FALSE,
-                    fileName=paste(pathReport, "Summary.txt", sep=""))
-  printTextProtocol(tests, showDetails=TRUE,
-                    fileName=paste(pathReport, ".txt", sep=""))
- 
-  ## Report to HTML file
-  printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
- 
-  ## Return stop() to cause R CMD check stop in case of
-  ##  - failures i.e. FALSE to unit tests or
-  ##  - errors i.e. R errors
-  tmp <- getErrors(tests)
-  if(tmp$nFail > 0 | tmp$nErr > 0) {
-    stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
-               ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
-  }
-} else {
-  warning("cannot run unit tests -- package RUnit is not available")
-}
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 00000000..01c9b7cd
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(mkin)
+
+test_check("mkin")
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
new file mode 100644
index 00000000..ce1e0a5a
--- /dev/null
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -0,0 +1,58 @@
+# Copyright (C) 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/>
+
+context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
+
+SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                   m1 = list(type = "SFO"))
+SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                      m1 = list(type = "SFO"), 
+                      use_of_ff = "max")
+
+fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
+
+# Results are from p. 40
+
+test_that("Fitted parameters are correct for FOCUS D", {
+  expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), 
+                    c(99.60, 0.0987, 0.0053, 0.5145))
+})
+
+test_that("FOCUS chi2 error levels are correct for FOCUS D", {
+  expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), 
+                    c(6.40, 6.46, 4.69))
+})
+
+test_that("DT50/90 are correct for FOCUS D when using formation fractions", {
+  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), 
+               c(7.02, 23.33))
+  expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), 
+               c(131.8, 437.7))
+})
+
+test_that("DT50/90 are correct for FOCUS D when not using formation fractions", {
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), 
+               c(7.02, 23.33))
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), 
+               c(131.8, 437.7))
+})
+
+# References:
+# Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+# zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R
new file mode 100644
index 00000000..65e1ada7
--- /dev/null
+++ b/tests/testthat/test_FOCUS_chi2_error_level.R
@@ -0,0 +1,53 @@
+# Copyright (C) 2014-15 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/>
+
+# These tests were migrated from inst/unitTests/runit.mkinerrmin.R
+
+context("Calculation of FOCUS chi2 error levels")
+
+SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                      m1 = list(type = "SFO"), 
+                      use_of_ff = "max")
+
+test_that("Chi2 error levels for FOCUS D are as in mkin 0.9-33", {
+
+  fit <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
+
+  errmin.FOCUS_2006_D_rounded = data.frame(
+    err.min = c(0.0640, 0.0646, 0.0469),
+    n.optim = c(4, 2, 2),
+    df = c(15, 7, 8), 
+    row.names = c("All data", "parent", "m1"))
+
+  expect_equal(round(mkinerrmin(fit), 4),
+               errmin.FOCUS_2006_D_rounded)
+})
+
+test_that("Chi2 error levels for FOCUS E are as in mkin 0.9-33", {
+
+  fit <- mkinfit(SFO_SFO.ff, FOCUS_2006_E, quiet = TRUE)
+
+  errmin.FOCUS_2006_E_rounded = data.frame(
+    err.min = c(0.1544, 0.1659, 0.1095),
+    n.optim = c(4, 2, 2),
+    df = c(13, 7, 6),
+    row.names = c("All data", "parent", "m1"))
+
+  expect_equal(round(mkinerrmin(fit), 4),
+               errmin.FOCUS_2006_E_rounded)
+})
diff --git a/inst/unitTests/runit.mkinpredict.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
index 6635ea1f..1238bb28 100644
--- a/inst/unitTests/runit.mkinpredict.R
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -1,6 +1,6 @@
 # $Id: jranke $

 

-# Copyright (C) 2012 Johannes Ranke

+# Copyright (C) 2012-2015 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -18,48 +18,14 @@
 # You should have received a copy of the GNU General Public License along with

 # this program. If not, see <http://www.gnu.org/licenses/>

 

-# Check solution types for SFO {{{

-test.SFO_solution_types <- function()

-{

-  ot = seq(0, 100, by = 1)

-  SFO <- mkinmod(parent = list(type = "SFO"))

-  SFO.analytical <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

-        c(parent = 100), ot, solution_type = "analytical"), time == 100), digits=5)

-  SFO.deSolve <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

-        c(parent = 100), ot, solution_type = "deSolve"), time == 100), digits=5)

-  SFO.eigen <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

-        c(parent = 100), ot, solution_type = "eigen"), time == 100), digits=5)

-

-  checkEquals(SFO.analytical, SFO.deSolve)

-  checkEquals(SFO.analytical, SFO.eigen)

-} # }}}

-

-# Check solution types for FOMC {{{

-test.FOMC_solution_types <- function()

-{

-  ot = seq(0, 100, by = 1)

-  FOMC <- mkinmod(parent = list(type = "FOMC"))

-  FOMC.analytical <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),

-        c(parent = 100), ot, solution_type = "analytical"), time == 100), digits=5)

-  FOMC.deSolve <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),

-        c(parent = 100), ot, solution_type = "deSolve"), use_compiled = FALSE, time == 100), digits=5)

-  checkEquals(FOMC.analytical, FOMC.deSolve)

+# This was migrated from an RUnit test in inst/unitTests/runit.mkinpredict.R

 

-  if (require(ccSolve)) {

-    checkTrue(!is.null(FOMC$compiled))

-    FOMC.deSolve.compiled <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),

-          c(parent = 100), ot, solution_type = "deSolve"), time == 100), digits=5)

-    checkEquals(FOMC.analytical, FOMC.deSolve.compiled)

-  }

-

-} # }}}

-

-# Check model specification and solution types for SFO_SFO {{{

-# Relative Tolerance is 0.01%

-# Do not use time 0, as eigenvalue based solution does not give 0 at time 0 for metabolites

-# and relative tolerance is thus not met

-test.SFO_solution_types <- function()

-{

+context("Model predictions with mkinpredict")

+test_that("Variants of model predictions for SFO_SFO model give equivalent results", {

+  # Check model specification and solution types for SFO_SFO

+  # Relative Tolerance is 0.01%

+  # Do not use time 0, as eigenvalue based solution does not give 0 at time 0 for metabolites

+  # and relative tolerance is thus not met

   tol = 0.01

   SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"),

          m1 = list(type = "SFO"), use_of_ff = "min")

@@ -87,20 +53,18 @@ test.SFO_solution_types <- function()
   dev.1.e_d.percent = 100 * (r.1.e[-1] - r.1.d[-1])/r.1.e[-1]

   dev.1.e_d.percent = as.numeric(unlist((dev.1.e_d.percent)))

   dev.1.e_d.percent = ifelse(is.na(dev.1.e_d.percent), 0, dev.1.e_d.percent)

-  checkIdentical(dev.1.e_d.percent < tol, rep(TRUE, length(dev.1.e_d.percent)))

+  expect_equivalent(dev.1.e_d.percent < tol, rep(TRUE, length(dev.1.e_d.percent)))

 

   # Compare eigen and deSolve for maximum use of formation fractions

-  dev.2.e_d.percent = 100 * (r.2.e[-1] - r.2.d[-1])/r.2.e[-1]

+  dev.2.e_d.percent = 100 * (r.1.e[-1] - r.1.d[-1])/r.1.e[-1]

   dev.2.e_d.percent = as.numeric(unlist((dev.2.e_d.percent)))

   dev.2.e_d.percent = ifelse(is.na(dev.2.e_d.percent), 0, dev.2.e_d.percent)

-  checkIdentical(dev.2.e_d.percent < tol, rep(TRUE, length(dev.2.e_d.percent)))

+  expect_equivalent(dev.2.e_d.percent < tol, rep(TRUE, length(dev.2.e_d.percent)))

 

   # Compare minimum and maximum use of formation fractions

   dev.1_2.e.percent = 100 * (r.1.e[-1] - r.2.e[-1])/r.1.e[-1]

   dev.1_2.e.percent = as.numeric(unlist((dev.1_2.e.percent)))

   dev.1_2.e.percent = ifelse(is.na(dev.1_2.e.percent), 0, dev.1_2.e.percent)

-  checkIdentical(dev.1_2.e.percent < tol, rep(TRUE, length(dev.1_2.e.percent)))

-

-} # }}}

+  expect_equivalent(dev.1_2.e.percent < tol, rep(TRUE, length(dev.1_2.e.percent)))

 

-# vim: set foldmethod=marker ts=2 sw=2 expandtab:

+})

diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R
new file mode 100644
index 00000000..5dcf297c
--- /dev/null
+++ b/tests/testthat/test_parent_only.R
@@ -0,0 +1,211 @@
+# Copyright (C) 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/>
+
+context("Fitting of parent only models")
+
+calc_dev.percent <- function(fitlist, reference, endpoints = TRUE, round_results = NULL) {
+  dev.percent <- list()
+  for (i in 1:length(fitlist)) {
+    fit <- fitlist[[i]]
+    if (endpoints) {
+      results <- c(fit$bparms.optim, 
+                   endpoints(fit)$distimes$DT50,
+                   endpoints(fit)$distimes$DT90)
+    } else {
+      results <- fit$bparms.optim
+    }
+    if (!missing(round_results)) results <- round(results, round_results)
+    dev.percent[[i]] <- abs(100 * ((reference - results)/reference))
+  }
+  return(dev.percent)
+}
+
+SFO <- mkinmod(parent = list(type = "SFO"))
+FOMC <- mkinmod(parent = list(type = "FOMC"))
+DFOP <- mkinmod(parent = list(type = "DFOP"))
+HS <- mkinmod(parent = list(type = "HS"))
+SFORB <- mkinmod(parent = list(type = "SFORB"))
+
+test_that("Fits for FOCUS A deviate less than 0.1% from median of values from FOCUS report", {
+  fit.A.SFO <- list(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
+
+  median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, 
+                                        dataset == "A", 
+                                        c(M0, k, DT50, DT90)), "median"))
+
+  dev.percent.A.SFO <- calc_dev.percent(fit.A.SFO, median.A.SFO)
+  expect_equivalent(dev.percent.A.SFO[[1]] < 0.1, rep(TRUE, 4))
+
+  # Fitting FOCUS A with FOMC is possible, but the correlation between
+  # alpha and beta, when obtained, is 1.0000, and the fit sometimes failed on
+  # Windows, as the Port algorithm did not converge (winbuilder, 2015-05-15)
+  fit.A.FOMC <- try(list(mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)))
+  if (!inherits(fit.A.FOMC, "try-error")) {
+
+    median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, 
+                                          dataset == "A", 
+                                          c(M0, alpha, beta, DT50, DT90)), "median"))
+
+    dev.percent.A.FOMC <- calc_dev.percent(fit.A.FOMC, median.A.FOMC)
+    # alpha and are beta ill-determined, do not compare those
+    expect_equivalent(dev.percent.A.FOMC[[1]][c(1, 4, 5)] < 0.1, rep(TRUE, 3))
+  }
+
+  fit.A.DFOP <- list(mkinfit("DFOP", FOCUS_2006_A, quiet = TRUE))
+
+  median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, 
+                                        dataset == "A", 
+                                        c(M0, k1, k2, f, DT50, DT90)), "median"))
+
+  dev.percent.A.DFOP <- calc_dev.percent(fit.A.DFOP, median.A.DFOP)
+  #expect_equivalent(dev.percent.A.DFOP[[1]] < 0.1, rep(TRUE, 6)) # g/f is ill-determined
+  expect_equivalent(dev.percent.A.DFOP[[1]][c(1, 2, 3, 5, 6)] < 0.1, rep(TRUE, 5))
+
+  fit.A.HS <- list(mkinfit("HS", FOCUS_2006_A, quiet = TRUE))
+
+  median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, 
+                                        dataset == "A", 
+                                        c(M0, k1, k2, tb, DT50, DT90)), "median"))
+
+  dev.percent.A.HS <- calc_dev.percent(fit.A.HS, median.A.HS)
+  expect_equivalent(dev.percent.A.HS[[1]] < 0.1, rep(TRUE, 6))
+})
+
+test_that("Fits for FOCUS B deviate less than 0.1% from median of values from FOCUS report", {
+  fit.B.SFO <- list(mkinfit("SFO", FOCUS_2006_B, quiet = TRUE))
+
+  median.B.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, 
+                                        dataset == "B", 
+                                        c(M0, k, DT50, DT90)), "median"))
+
+  dev.percent.B.SFO <- calc_dev.percent(fit.B.SFO, median.B.SFO)
+  expect_equivalent(dev.percent.B.SFO[[1]] < 0.1, rep(TRUE, 4))
+
+  fit.B.FOMC <- list(mkinfit("FOMC", FOCUS_2006_B, quiet = TRUE))
+
+  median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, 
+                                        dataset == "B", 
+                                        c(M0, alpha, beta, DT50, DT90)), "median"))
+
+  dev.percent.B.FOMC <- calc_dev.percent(fit.B.FOMC, median.B.FOMC)
+  expect_equivalent(dev.percent.B.FOMC[[1]] < 0.1, rep(TRUE, 5))
+
+  fit.B.DFOP <- list(mkinfit("DFOP", FOCUS_2006_B, quiet = TRUE))
+
+  median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, 
+                                        dataset == "B", 
+                                        c(M0, k1, k2, f, DT50, DT90)), "median"))
+
+  dev.percent.B.DFOP <- calc_dev.percent(fit.B.DFOP, median.B.DFOP)
+  #expect_equivalent(dev.percent.B.DFOP[[1]] < 0.1, rep(TRUE, 6)) # g/f is ill-determined
+  expect_equivalent(dev.percent.B.DFOP[[1]][c(1, 2, 3, 5, 6)] < 0.1, rep(TRUE, 5))
+
+  fit.B.HS <- list(mkinfit("HS", FOCUS_2006_B, quiet = TRUE))
+
+  median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, 
+                                        dataset == "B", 
+                                        c(M0, k1, k2, tb, DT50, DT90)), 
+                                   "median", na.rm = TRUE))
+
+  dev.percent.B.HS <- calc_dev.percent(fit.B.HS, median.B.HS)
+  expect_equivalent(dev.percent.B.HS[[1]] < 0.1, rep(TRUE, 6))
+
+  fit.B.SFORB <- list(mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE))
+  dev.percent.B.SFORB <- calc_dev.percent(fit.B.SFORB, median.B.DFOP)
+  expect_equivalent(dev.percent.B.SFORB[[1]][c(1, 5, 6)] < 0.1, rep(TRUE, 3))
+})
+
+test_that("Fits for FOCUS C deviate less than 0.1% from median of values from FOCUS report", {
+  fit.C.SFO <- list(mkinfit("SFO", FOCUS_2006_C, quiet = TRUE))
+
+  median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, 
+                                        dataset == "C", 
+                                        c(M0, k, DT50, DT90)), "median"))
+
+  dev.percent.C.SFO <- calc_dev.percent(fit.C.SFO, median.C.SFO)
+  expect_equivalent(dev.percent.C.SFO[[1]] < 0.1, rep(TRUE, 4))
+
+  fit.C.FOMC <- list(mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE))
+
+  median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, 
+                                        dataset == "C", 
+                                        c(M0, alpha, beta, DT50, DT90)), "median"))
+
+  dev.percent.C.FOMC <- calc_dev.percent(fit.C.FOMC, median.C.FOMC, 
+                                         round_results = 2) # Not enough precision in FOCUS results
+  expect_equivalent(dev.percent.C.FOMC[[1]] < 0.1, rep(TRUE, 5))
+
+  fit.C.HS <- list(mkinfit("HS", FOCUS_2006_C, quiet = TRUE))
+
+  median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, 
+                                        dataset == "C", 
+                                        c(M0, k1, k2, tb, DT50, DT90)), "median"))
+
+  dev.percent.C.HS <- calc_dev.percent(fit.C.HS, median.C.HS, round_results = c(2, 4, 6, 2, 2))
+  # Not enouth precision in k2 available
+  expect_equivalent(dev.percent.C.HS[[1]] < c(0.1, 0.1, 0.3, 0.1, 0.1, 0.1), rep(TRUE, 6))
+})
+
+test_that("SFO fits give approximately (0.001%) equal results with different solution methods", {
+  fit.A.SFO.default <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)$bparms.optim
+
+  fits.A.SFO <- list()
+  fits.A.SFO[[1]] <- mkinfit(SFO, FOCUS_2006_A, quiet = TRUE)
+  fits.A.SFO[[2]] <- mkinfit(SFO, FOCUS_2006_A, quiet = TRUE, solution_type = "eigen")
+  fits.A.SFO[[3]] <- mkinfit(SFO, FOCUS_2006_A, quiet = TRUE, solution_type = "deSolve")
+
+  dev.percent <- calc_dev.percent(fits.A.SFO, fit.A.SFO.default, endpoints = FALSE)
+  expect_equivalent(dev.percent[[1]] < 0.001, rep(TRUE, 2))
+  expect_equivalent(dev.percent[[2]] < 0.001, rep(TRUE, 2))
+  expect_equivalent(dev.percent[[3]] < 0.001, rep(TRUE, 2))
+})
+
+test_that("FOMC fits give approximately (0.001%) equal results with different solution methods", {
+  fit.C.FOMC.default <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)$bparms.optim
+
+  fits.C.FOMC <- list()
+  fits.C.FOMC[[1]] <- mkinfit(FOMC, FOCUS_2006_C, quiet = TRUE)
+  fits.C.FOMC[[2]] <- mkinfit(FOMC, FOCUS_2006_C, quiet = TRUE, solution_type = "deSolve")
+
+  dev.percent <- calc_dev.percent(fits.C.FOMC, fit.C.FOMC.default, endpoints = FALSE)
+  expect_equivalent(dev.percent[[1]] < 0.001, rep(TRUE, 3))
+  expect_equivalent(dev.percent[[2]] < 0.001, rep(TRUE, 3))
+})
+
+test_that("DFOP fits give approximately (0.001%) equal results with different solution methods", {
+  fit.C.DFOP.default <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)$bparms.optim
+
+  fits.C.DFOP <- list()
+  fits.C.DFOP[[1]] <- mkinfit(DFOP, FOCUS_2006_C, quiet = TRUE)
+  fits.C.DFOP[[2]] <- mkinfit(DFOP, FOCUS_2006_C, quiet = TRUE, solution_type = "deSolve")
+
+  dev.percent <- calc_dev.percent(fits.C.DFOP, fit.C.DFOP.default, endpoints = FALSE)
+  expect_equivalent(dev.percent[[1]] < 0.001, rep(TRUE, 4))
+  expect_equivalent(dev.percent[[2]] < 0.001, rep(TRUE, 4))
+})
+
+test_that("SFORB fits give approximately (0.002%) equal results with different solution methods", {
+  fit.B.SFORB.default <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE)$bparms.optim
+
+  fits.B.SFORB <- list()          
+  fits.B.SFORB[[1]] <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE, solution_type = "eigen")
+  fits.B.SFORB[[2]] <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE, solution_type = "deSolve")
+  dev.percent <- calc_dev.percent(fits.B.SFORB, fit.B.SFORB.default, endpoints = FALSE)
+  expect_equivalent(dev.percent[[1]] < 0.001, rep(TRUE, 4))
+  expect_equivalent(dev.percent[[2]] < 0.002, rep(TRUE, 4))
+})
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)

+})

diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
new file mode 100644
index 00000000..2bf01075
--- /dev/null
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R
@@ -0,0 +1,67 @@
+# Copyright (C) 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/>
+
+context("Results for synthetic data established in expertise for UBA (Ranke 2014)")
+
+
+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
+                           M1 = list(type = "SFO", to = "M2"),
+                           M2 = list(type = "SFO"), use_of_ff = "max")
+
+
+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")),
+                            M1 = list(type = "SFO"),
+                            M2 = list(type = "SFO"), use_of_ff = "max")
+
+fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, 
+                         synthetic_data_for_UBA_2014[[1]]$data, 
+                         quiet = TRUE)
+fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
+                          synthetic_data_for_UBA_2014[[12]]$data,
+                          quiet = TRUE)
+
+# Results for SFO_lin_a from p. 48
+
+test_that("Fitted parameters are correct for SFO_lin_a", {
+  parms <- round(fit_SFO_lin_a$bparms.optim, c(1, 4, 4, 4, 4, 4))
+  expect_equivalent(parms, c(102.1, 0.7393, 0.2992, 0.0202, 0.7687, 0.7229))
+})
+
+test_that("FOCUS chi2 error levels are correct for SFO_lin_a", {
+  errmin <- round(100 * mkinerrmin(fit_SFO_lin_a)$err.min, 2)
+  expect_equivalent(errmin, c(8.45, 8.66, 10.58, 3.59))
+})
+
+# Results for DFOP_par_c from p. 54
+
+test_that("Fitted parameters are correct for DFOP_par_c", {
+  parms <- round(fit_DFOP_par_c$bparms.optim, c(1, 4, 4, 4, 4, 4, 4, 4))
+  expect_equal(parms, c(parent_0 = 103.0, 
+                        k_M1 = 0.0389, k_M2 = 0.0095,
+                        f_parent_to_M1 = 0.5565, f_parent_to_M2 = 0.3784,
+                        k1 = 0.3263, k2 = 0.0202, g = 0.7130))
+})
+
+test_that("FOCUS chi2 error levels are correct for DFOP_par_c", {
+  errmin <- round(100 * mkinerrmin(fit_DFOP_par_c)$err.min, 2)
+  expect_equivalent(errmin, c(4.03, 3.05, 5.07, 3.17))
+})
+
+# References:
+# Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+# zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index f8fd354f..3174a23a 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f83f8735..8f1e0884 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf