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-rw-r--r--.gitignore2
-rw-r--r--DESCRIPTION6
-rw-r--r--GNUmakefile9
-rw-r--r--NEWS.md7
-rw-r--r--data/synthetic_data_for_UBA_2014.RDatabin0 -> 2243 bytes
-rw-r--r--inst/unitTests/Makefile15
-rw-r--r--inst/unitTests/runit.mkinerrmin.R79
-rw-r--r--inst/unitTests/runit.mkinfit.R239
-rw-r--r--man/synthetic_data_for_UBA.Rd65
-rw-r--r--tests/doRUnit.R42
-rw-r--r--tests/testthat.R4
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R58
-rw-r--r--tests/testthat/test_FOCUS_chi2_error_level.R53
-rw-r--r--tests/testthat/test_mkinpredict_SFO_SFO.R (renamed from inst/unitTests/runit.mkinpredict.R)62
-rw-r--r--tests/testthat/test_parent_only.R211
-rw-r--r--tests/testthat/test_schaefer07_complex_case.R68
-rw-r--r--tests/testthat/test_synthetic_data_for_UBA_2014.R67
-rw-r--r--vignettes/FOCUS_Z.pdfbin214499 -> 215014 bytes
-rw-r--r--vignettes/mkin.pdfbin160335 -> 160260 bytes
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 $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/
submit:
- @echo "\nHow about make test, make check, make winbuilder and make r-forge?"
+ @echo "\nHow about make test, make check, make winbuilder"
@echo "\nIs the DESCRIPTION file up to date?"
+ @echo "\nIs the NEWS.md file up to date?"
@echo "\nAre you sure you want to release to CRAN?"
- @echo "\nThen use the form at http://cran.r-project.org/submit.html"
+ @echo "\nThen make r-forge, commit leftover changes if any, tag the release and use the form at http://cran.r-project.org/submit.html"
diff --git a/NEWS.md b/NEWS.md
index 023f3645..de3b0400 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,10 @@
# CHANGES in mkin VERSION 0.9-35
+## MAJOR CHANGES
+
+- Switch from RUnit to testthat for testing
+
## BUG FIXES
- `mkinparplot()`: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit
@@ -23,6 +27,9 @@
## NEW FEATURES
- `mkinfit()`: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.
+- A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.
+- Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA
+- Add tests based on these datasets
# CHANGES in mkin VERSION 0.9-34
diff --git a/data/synthetic_data_for_UBA_2014.RData b/data/synthetic_data_for_UBA_2014.RData
new file mode 100644
index 00000000..12132c97
--- /dev/null
+++ b/data/synthetic_data_for_UBA_2014.RData
Binary files differ
diff --git a/inst/unitTests/Makefile b/inst/unitTests/Makefile
deleted file mode 100644
index 8d132253..00000000
--- a/inst/unitTests/Makefile
+++ /dev/null
@@ -1,15 +0,0 @@
-TOP=../..
-PKG=${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
Binary files differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f83f8735..8f1e0884 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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