Start of migration from RUnit to testthat

10 files changed, 58 insertions, 61 deletions

diff --git a/.gitignore b/.gitignore
index 39eac04e..81a0b7d7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -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))
+})