Merge branch 'master' into compile_odes

Conflicts
(resolved manually, deleting code that I had
integrated into the RUnit tests for testing the
compiled version):
	.gitignore
	DESCRIPTION
	inst/unitTests/runit.mkinerrmin.R
	inst/unitTests/runit.mkinfit.R
	tests/testthat/test_mkinpredict_SFO_SFO.R
	vignettes/FOCUS_L.html

6 files changed, 527 insertions, 0 deletions

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/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
new file mode 100644
index 00000000..1238bb28
--- /dev/null
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -0,0 +1,70 @@
+# $Id: jranke $

+

+# Copyright (C) 2012-2015 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 was migrated from an RUnit test in inst/unitTests/runit.mkinpredict.R

+

+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")

+  SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),

+         m1 = list(type = "SFO"), use_of_ff = "max")

+

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

+  r.1.e <- subset(mkinpredict(SFO_SFO.1, 

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

+             c(parent = 100, m1 = 0), ot, solution_type = "eigen"), 

+                 time %in% c(1, 10, 50, 100))

+  r.1.d <- subset(mkinpredict(SFO_SFO.1, 

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

+             c(parent = 100, m1 = 0), ot, solution_type = "deSolve"), 

+                 time %in% c(1, 10, 50, 100))

+

+  r.2.e <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

+	    c(parent = 100, m1 = 0), ot, solution_type = "eigen"),

+                  time %in% c(1, 10, 50, 100))

+  r.2.d <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

+	    c(parent = 100, m1 = 0), ot, solution_type = "deSolve"),

+                  time %in% c(1, 10, 50, 100))

+

+  # Compare eigen and deSolve for minimum use of formation fractions

+  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)

+  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.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)

+  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)

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

+

+})

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