diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | DESCRIPTION | 5 | ||||
| -rw-r--r-- | GNUmakefile | 4 | ||||
| -rw-r--r-- | inst/unitTests/Makefile | 15 | ||||
| -rw-r--r-- | tests/doRUnit.R | 42 | ||||
| -rw-r--r-- | tests/testthat.R | 4 | ||||
| -rw-r--r-- | tests/testthat/runit.mkinerrmin.R (renamed from inst/unitTests/runit.mkinerrmin.R) | 0 | ||||
| -rw-r--r-- | tests/testthat/runit.mkinfit.R (renamed from inst/unitTests/runit.mkinfit.R) | 0 | ||||
| -rw-r--r-- | tests/testthat/runit.mkinpredict.R (renamed from inst/unitTests/runit.mkinpredict.R) | 0 | ||||
| -rw-r--r-- | tests/testthat/test_parent_only.R | 48 |
10 files changed, 58 insertions, 61 deletions
@@ -9,4 +9,5 @@ vignettes/*.toc vignettes/.build.timestamp vignettes/mkin.tex vignettes/FOCUS_Z.tex +vignettes/compiled_models_cache mkin.Rcheck diff --git a/DESCRIPTION b/DESCRIPTION index 03976d1e..0477a200 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: 0.9-35 -Date: 2015-02-20 +Date: 2015-05-13 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), @@ -17,7 +17,8 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006). for a particular purpose. Depends: minpack.lm, rootSolve Imports: FME, deSolve -Suggests: knitr, RUnit +Suggests: knitr, + testthat License: GPL LazyLoad: yes LazyData: yes diff --git a/GNUmakefile b/GNUmakefile index 126dede1..b731166b 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')" 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 < ${SUITE} diff --git a/tests/doRUnit.R b/tests/doRUnit.R deleted file mode 100644 index 9faee940..00000000 --- a/tests/doRUnit.R +++ /dev/null @@ -1,42 +0,0 @@ -# Adapted from a version around 2.9 of the rcdk package by Rajarshi Guha -if(require("RUnit", quietly=TRUE)) { - - pkg <- "mkin" - path <- system.file(package=pkg, "unitTests") - - cat("\nRunning unit tests\n") - print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) - - library(package=pkg, character.only=TRUE) - - ## Define tests - testSuite <- defineTestSuite(name=paste(pkg, " Unit Tests"), - dirs=path) - ## Run - tests <- runTestSuite(testSuite) - - ## Default report name - pathReport <- file.path(path, "report") - - ## Report to stdout and text files - cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") - printTextProtocol(tests, showDetails=FALSE) - printTextProtocol(tests, showDetails=FALSE, - fileName=paste(pathReport, "Summary.txt", sep="")) - printTextProtocol(tests, showDetails=TRUE, - fileName=paste(pathReport, ".txt", sep="")) - - ## Report to HTML file - printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) - - ## Return stop() to cause R CMD check stop in case of - ## - failures i.e. FALSE to unit tests or - ## - errors i.e. R errors - tmp <- getErrors(tests) - if(tmp$nFail > 0 | tmp$nErr > 0) { - stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail, - ", #R errors: ", tmp$nErr, ")\n\n", sep="")) - } -} else { - warning("cannot run unit tests -- package RUnit is not available") -} diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 00000000..01c9b7cd --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(mkin) + +test_check("mkin") diff --git a/inst/unitTests/runit.mkinerrmin.R b/tests/testthat/runit.mkinerrmin.R index 56a33ff9..56a33ff9 100644 --- a/inst/unitTests/runit.mkinerrmin.R +++ b/tests/testthat/runit.mkinerrmin.R diff --git a/inst/unitTests/runit.mkinfit.R b/tests/testthat/runit.mkinfit.R index 8eefb995..8eefb995 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/tests/testthat/runit.mkinfit.R diff --git a/inst/unitTests/runit.mkinpredict.R b/tests/testthat/runit.mkinpredict.R index 997857ce..997857ce 100644 --- a/inst/unitTests/runit.mkinpredict.R +++ b/tests/testthat/runit.mkinpredict.R diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R new file mode 100644 index 00000000..16fc5131 --- /dev/null +++ b/tests/testthat/test_parent_only.R @@ -0,0 +1,48 @@ +context("Fitting of parent only models") + +calc_dev.percent <- function(fitlist, reference) { + for (i in 1:length(fitlist)) { + fit <- fitlist[[i]] + results <- c(fit$bparms.optim, + endpoints(fit)$distimes$DT50, + endpoints(fit)$distimes$DT90) + dev.percent[[i]] <- abs(100 * ((reference - results)/reference)) + } + return(dev.percent) +} + +SFO <- mkinmod(parent = list(type = "SFO")) +FOMC <- mkinmod(parent = list(type = "FOMC")) + +test_that("SFO fit for FOCUS A deviates less than 0.1% from median of values from FOCUS report", { + 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) + fits.A.SFO[[3]] <- mkinfit(SFO, FOCUS_2006_A, quiet=TRUE, solution_type = "eigen") + fits.A.SFO[[4]] <- mkinfit(SFO, FOCUS_2006_A, quiet=TRUE, solution_type = "deSolve") + + median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, + dataset == "A", + c(M0, k, DT50, DT90)), "median")) + + dev.percent <- calc_dev.percent(fits.A.SFO, median.A.SFO) + expect_equivalent(dev.percent[[1]] < 0.1, rep(TRUE, 4)) + expect_equivalent(dev.percent[[2]] < 0.1, rep(TRUE, 4)) + expect_equivalent(dev.percent[[3]] < 0.1, rep(TRUE, 4)) + expect_equivalent(dev.percent[[4]] < 0.1, rep(TRUE, 4)) +}) + +test_that("SFO fit for FOCUS C deviates less than 0.1% from median of values from FOCUS report", { + fits.C.SFO <- list() + fits.C.SFO[[1]] <- mkinfit("SFO", FOCUS_2006_C, quiet=TRUE) + fits.C.SFO[[2]] <- mkinfit(SFO, FOCUS_2006_C, quiet=TRUE) + fits.C.SFO[[3]] <- mkinfit(SFO, FOCUS_2006_C, quiet=TRUE, solution_type = "deSolve") + + median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, + dataset == "C", + c(M0, k, DT50, DT90)), "median")) + dev.percent <- calc_dev.percent(fits.C.SFO, median.C.SFO) + expect_equivalent(dev.percent[[1]] < 0.1, rep(TRUE, 4)) + expect_equivalent(dev.percent[[2]] < 0.1, rep(TRUE, 4)) + expect_equivalent(dev.percent[[3]] < 0.1, rep(TRUE, 4)) +}) |