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-rw-r--r--test.log37
-rw-r--r--tests/testthat/FOCUS_2006_D.csf52
-rw-r--r--tests/testthat/FOCUS_2006_D.txt0
-rw-r--r--tests/testthat/test_CAKE_export.R51
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R2
-rw-r--r--tests/testthat/test_plots_summary_twa.R2
-rw-r--r--tests/testthat/test_plots_twa.R63
7 files changed, 129 insertions, 78 deletions
diff --git a/test.log b/test.log
index 4da96066..63f5b542 100644
--- a/test.log
+++ b/test.log
@@ -1,9 +1,15 @@
Loading mkin
Testing mkin
✔ | OK F W S | Context
- ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.5 s]
- ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.2 s]
- ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [16.3 s]
+ ⠏ | 0 | Export dataset for reading into CAKE ⠋ | 1 | Export dataset for reading into CAKE ⠙ | 1 1 | Export dataset for reading into CAKE ⠙ | 2 | Export dataset for reading into CAKE ⠹ | 3 | Export dataset for reading into CAKE ⠸ | 4 | Export dataset for reading into CAKE ⠼ | 5 | Export dataset for reading into CAKE ⠴ | 6 | Export dataset for reading into CAKE ⠦ | 7 | Export dataset for reading into CAKE ⠧ | 8 | Export dataset for reading into CAKE ⠇ | 8 1 | Export dataset for reading into CAKE ✔ | 8 1 | Export dataset for reading into CAKE [1.4 s]
+────────────────────────────────────────────────────────────────────────────────
+test_CAKE_export.R:50: skip: Test data from Appendix D are correctly evaluated
+Figure not generated yet: plot-nafta-analysis.svg
+Please run `vdiffr::manage_cases()` to validate the figure.
+────────────────────────────────────────────────────────────────────────────────
+ ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.2 s]
+ ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.8 s]
+ ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [15.9 s]
────────────────────────────────────────────────────────────────────────────────
test_irls.R:48: skip: Reweighting method 'tc' works
Too much trouble with datasets that are randomly generated
@@ -14,20 +20,23 @@ test_logistic.R:41: skip: The logistic fit can be done via differential equation
Skip slow fit of logistic model using deSolve without compilation
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | Model predictions with mkinpredict ⠋ | 1 | Model predictions with mkinpredict ⠙ | 2 | Model predictions with mkinpredict ⠹ | 3 | Model predictions with mkinpredict ✔ | 3 | Model predictions with mkinpredict [0.3 s]
- ⠏ | 0 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 1 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ✔ | 9 | Evaluations according to 2015 NAFTA guidance [0.9 s]
- ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [24.1 s]
- ⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ⠼ | 5 | Calculation of maximum time weighted average concentrations (TWAs) ⠴ | 6 | Calculation of maximum time weighted average concentrations (TWAs) ⠦ | 7 | Calculation of maximum time weighted average concentrations (TWAs) ⠧ | 8 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 8 | Calculation of maximum time weighted average concentrations (TWAs) [7.3 s]
- ⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary
- ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ✔ | 3 | Plotting [0.3 s]
+ ⠏ | 0 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 1 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ✔ | 9 | Evaluations according to 2015 NAFTA guidance [0.8 s]
+ ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [23.7 s]
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ⠼ | 5 | Calculation of maximum time weighted average concentrations (TWAs) ⠴ | 6 | Calculation of maximum time weighted average concentrations (TWAs) ⠦ | 7 | Calculation of maximum time weighted average concentrations (TWAs) ⠧ | 8 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 8 | Calculation of maximum time weighted average concentrations (TWAs) [7.2 s]
- ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ✔ | 3 | Plotting [0.2 s]
- ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [6.0 s]
- ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.5 s]
+ ⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary
+ ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 1 1 | Plotting ⠹ | 2 1 | Plotting ⠸ | 3 1 | Plotting ✔ | 3 1 | Plotting [0.3 s]
+────────────────────────────────────────────────────────────────────────────────
+test_plots_summary_twa.R:76: skip: Plotting mmkin objects is reproducible
+Figure not generated yet: mkinparplot-for-focus-c-sfo.svg
+Please run `vdiffr::manage_cases()` to validate the figure.
+────────────────────────────────────────────────────────────────────────────────
+ ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s]
+ ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.3 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 83.6 s
+Duration: 74.6 s
-OK: 80
+OK: 77
Failed: 0
Warnings: 0
-Skipped: 2
+Skipped: 4
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)
-})
-

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