diff options
-rw-r--r-- | .gitignore | 2 | ||||
-rw-r--r-- | DESCRIPTION | 6 | ||||
-rw-r--r-- | GNUmakefile | 9 | ||||
-rw-r--r-- | NEWS.md | 7 | ||||
-rw-r--r-- | data/synthetic_data_for_UBA_2014.RData | bin | 0 -> 2243 bytes | |||
-rw-r--r-- | inst/unitTests/Makefile | 15 | ||||
-rw-r--r-- | inst/unitTests/runit.mkinerrmin.R | 79 | ||||
-rw-r--r-- | inst/unitTests/runit.mkinfit.R | 239 | ||||
-rw-r--r-- | man/synthetic_data_for_UBA.Rd | 65 | ||||
-rw-r--r-- | tests/doRUnit.R | 42 | ||||
-rw-r--r-- | tests/testthat.R | 4 | ||||
-rw-r--r-- | tests/testthat/test_FOCUS_D_UBA_expertise.R | 58 | ||||
-rw-r--r-- | tests/testthat/test_FOCUS_chi2_error_level.R | 53 | ||||
-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.R | 211 | ||||
-rw-r--r-- | tests/testthat/test_schaefer07_complex_case.R | 68 | ||||
-rw-r--r-- | tests/testthat/test_synthetic_data_for_UBA_2014.R | 67 | ||||
-rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 214499 -> 215014 bytes | |||
-rw-r--r-- | vignettes/mkin.pdf | bin | 160335 -> 160260 bytes |
19 files changed, 556 insertions, 431 deletions
@@ -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 $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/ submit: - @echo "\nHow about make test, make check, make winbuilder and make r-forge?" + @echo "\nHow about make test, make check, make winbuilder" @echo "\nIs the DESCRIPTION file up to date?" + @echo "\nIs the NEWS.md file up to date?" @echo "\nAre you sure you want to release to CRAN?" - @echo "\nThen use the form at http://cran.r-project.org/submit.html" + @echo "\nThen make r-forge, commit leftover changes if any, tag the release and use the form at http://cran.r-project.org/submit.html" @@ -13,6 +13,10 @@ # CHANGES in mkin VERSION 0.9-35 +## MAJOR CHANGES + +- Switch from RUnit to testthat for testing + ## BUG FIXES - `mkinparplot()`: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit @@ -23,6 +27,9 @@ ## NEW FEATURES - `mkinfit()`: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting. +- A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added. +- Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA +- Add tests based on these datasets # CHANGES in mkin VERSION 0.9-34 diff --git a/data/synthetic_data_for_UBA_2014.RData b/data/synthetic_data_for_UBA_2014.RData Binary files differnew file mode 100644 index 00000000..12132c97 --- /dev/null +++ b/data/synthetic_data_for_UBA_2014.RData diff --git a/inst/unitTests/Makefile b/inst/unitTests/Makefile deleted file mode 100644 index 8d132253..00000000 --- a/inst/unitTests/Makefile +++ /dev/null @@ -1,15 +0,0 @@ -TOP=../.. -PKG=${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 Binary files differindex f8fd354f..3174a23a 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex f83f8735..8f1e0884 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |