Test CAKE export

6 files changed, 106 insertions, 64 deletions

diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
new file mode 100644
index 00000000..d695e90d
--- /dev/null
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -0,0 +1,52 @@
+[FileInfo]
+CAKE-Version: 3.3 (Release)
+Name: FOCUS 2006 D
+Description: 
+MeasurementUnits: % AR
+TimeUnits: days
+Comments: Created using mkin::CAKE_export
+Date: 2019-02-25
+Optimiser: IRLS
+
+[Data]
+NewDataSet: FOCUS C
+Time	Parent
+0	85.1
+1	57.9
+3	29.9
+7	14.6
+14	9.7
+28	6.6
+63	4
+91	3.9
+119	0.6
+
+NewDataSet: FOCUS D
+Time	Parent	M1
+0	99.46	0
+0	102.04	0
+1	93.5	4.84
+1	92.5	5.64
+3	63.23	12.91
+3	68.99	12.96
+7	52.32	22.97
+7	55.13	24.47
+14	27.27	41.69
+14	26.64	33.21
+21	11.5	44.37
+21	11.64	46.44
+35	2.85	41.22
+35	2.91	37.95
+50	0.69	41.19
+50	0.63	40.01
+75	0.05	40.09
+75	0.06	33.85
+100		31.04
+100		33.13
+120		25.15
+120		33.31
+
+
+[ComponentNames]
+Parent:parent
+M1:m1
diff --git a/tests/testthat/FOCUS_2006_D.txt b/tests/testthat/FOCUS_2006_D.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/tests/testthat/FOCUS_2006_D.txt
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
new file mode 100644
index 00000000..aeb192c8
--- /dev/null
+++ b/tests/testthat/test_CAKE_export.R
@@ -0,0 +1,51 @@
+# Copyright (C) 2019 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("Export dataset for reading into CAKE")
+
+test_that("Exporting is reproducible", {
+  CAKE_export(list("FOCUS C" = FOCUS_2006_C,
+                   "FOCUS D" = FOCUS_2006_D),
+    map = c(parent = "Parent", m1 = "M1"),
+    filename = "FOCUS_2006_D.csf", overwrite = TRUE, 
+    study = "FOCUS 2006 D")
+  csf <- readLines(con = "FOCUS_2006_D.csf")
+  expect_known_output(csf, "FOCUS_2006_D.txt")
+})
+
+test_that("Test data from Appendix D are correctly evaluated", {
+  expect_message(res <- nafta(MRID_555555, "MRID 555555"))
+
+  # From Figure D.1
+  dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2)
+  expect_equivalent(res$distimes[, 1:2], dtx_sop, tolerance = 1,
+                    scale = 1)
+
+  C0_sop <- c(SFO = 83.8, IORE = 96.9, DFOP = 97.6)
+  C0_mkin <- sapply(res$parameters, function(x) x["parent_0", "Estimate"])
+  expect_equivalent(C0_mkin, C0_sop, scale = 1, tolerance = 0.1)
+
+  expect_equal(round(res$S_c), 717)
+  expect_equal(signif(res$S[["SFO"]], 3), 1.38e+3)
+  expect_equal(round(res$t_rep), 841)
+
+  expect_known_output(print(res), "print_nafta_analysis.txt")
+
+  plot_nafta <- function() plot(res)
+  vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)
+})
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 74097afa..42c4fcfb 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015,2018 Johannes Ranke
+# Copyright (C) 2015,2019 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index d5f4f199..5201567d 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -68,10 +68,12 @@ context("Plotting")
 test_that("Plotting mmkin objects is reproducible", {
   skip_on_cran()
   plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[["SFO", "FOCUS_C"]])
+  mkinparplot_FOCUS_C_SFO <- function() mkinparplot(fits[["SFO", "FOCUS_C"]])
   mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
   mmkin_SFO <- function() plot(fits["SFO",])
 
   vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
+  vdiffr::expect_doppelganger("mkinparplot for FOCUS C SFO", mkinparplot_FOCUS_C_SFO)
   vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
   vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
 })
diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
deleted file mode 100644
index ff899bc9..00000000
--- a/tests/testthat/test_plots_twa.R
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright (C) 2016-2019 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/>
-
-models <- c("SFO", "FOMC", "DFOP", "HS")
-fits <- mmkin(models,
-  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
-  quiet = TRUE, cores = if (Sys.getenv("TRAVIS") == "") 15 else 1)
-
-context("Calculation of maximum time weighted average concentrations (TWAs)")
-
-test_that("Time weighted average concentrations are correct", {
-  skip_on_cran()
-
-  outtimes_10 <- seq(0, 10, length.out = 10000)
-
-  for (ds in c("FOCUS_C", "FOCUS_D")) {
-    for (model in models) {
-      fit <- fits[[model, ds]]
-      bpar <- summary(fit)$bpar[, "Estimate"]
-      pred_10 <- mkinpredict(fit$mkinmod,
-                  odeparms = bpar[2:length(bpar)],
-                  odeini = c(parent = bpar[[1]]),
-                  outtimes = outtimes_10)
-      twa_num <- mean(pred_10$parent)
-      names(twa_num) <- 10
-      twa_ana <- max_twa_parent(fit, 10)
-
-      # Test for absolute difference (scale = 1)
-      # The tolerance can be reduced if the length of outtimes is increased,
-      # but this needs more computing time so we stay with lenght.out = 10k
-      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
-    }
-  }
-})
-
-context("Plotting")
-
-test_that("Plotting mmkin objects is reproducible", {
-  skip_on_cran()
-  plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[["SFO", "FOCUS_C"]])
-  mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
-  mmkin_SFO <- function() plot(fits["SFO",])
-
-  vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
-  vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
-  vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
-})
-