From f7f92c29908550af82ac20041621c5b4404210d2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Feb 2019 17:33:49 +0100 Subject: Shorten path to test plot --- build.log | 3 - test.log | 18 +- .../plot-nafta-analysis.svg | 450 +++++++++++++++++++++ .../plot-nafta-analysis-sop-appendix-d.svg | 450 --------------------- tests/testthat/test_nafta.R | 4 +- 5 files changed, 461 insertions(+), 464 deletions(-) create mode 100644 tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg delete mode 100644 tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg diff --git a/build.log b/build.log index e7e1addc..6831459d 100644 --- a/build.log +++ b/build.log @@ -7,7 +7,4 @@ * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘mkin_0.9.48.1.tar.gz’ -Warnung in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L, - storing paths of more than 100 bytes is not portable: - ‘mkin/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg’ diff --git a/test.log b/test.log index df597cfa..ff374f43 100644 --- a/test.log +++ b/test.log @@ -1,9 +1,9 @@ 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 [2.4 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) ✔ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.1 s] - ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 1 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 1 1 | Iteratively reweighted least squares (IRLS) fitting [8.8 s] + ⠏ | 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) ✔ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.3 s] + ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 1 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 1 1 | Iteratively reweighted least squares (IRLS) fitting [8.9 s] ──────────────────────────────────────────────────────────────────────────────── test_irls.R:44: skip: Reweighting method 'tc' works Too much trouble with datasets that are randomly generated @@ -14,18 +14,18 @@ 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 the NAFTA guidance from 2015 ⠋ | 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 1 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 2 | Evaluations according to the NAFTA guidance from 2015 ⠹ | 3 | Evaluations according to the NAFTA guidance from 2015 ⠸ | 4 | Evaluations according to the NAFTA guidance from 2015 ⠼ | 5 | Evaluations according to the NAFTA guidance from 2015 ⠴ | 6 | Evaluations according to the NAFTA guidance from 2015 ⠦ | 7 | Evaluations according to the NAFTA guidance from 2015 ⠧ | 8 | Evaluations according to the NAFTA guidance from 2015 ⠇ | 9 | Evaluations according to the NAFTA guidance from 2015 ✔ | 9 | Evaluations according to the NAFTA guidance from 2015 [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 [23.9 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 | 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 [24.3 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 | 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) [7.8 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) [7.4 s] ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ✔ | 3 | Plotting [0.3 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 [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) [7.4 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] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 75.0 s +Duration: 75.7 s OK: 74 Failed: 0 diff --git a/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg b/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg new file mode 100644 index 00000000..58f57e93 --- /dev/null +++ b/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg @@ -0,0 +1,450 @@ + + + + + + + + + + + +0 +100 +200 +300 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + +Time +Observed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +MRID 555555 +SFO + +χ +2 + +error level += +9.04% + + + + + + + + + + + + + + + + +0 +100 +200 +300 +400 + + + + + + +-20 +-10 +0 +10 +20 + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +SFO residuals + + + + + + + + + + + + + + + +0 +100 +200 +300 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + +Time +Observed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +MRID 555555 +IORE + +χ +2 + +error level += +5.65% + + + + + + + + + + + + + + + + +0 +100 +200 +300 +400 + + + + + + +-20 +-10 +0 +10 +20 + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +IORE residuals + + + + + + + + + + + + + + + +0 +100 +200 +300 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + +Time +Observed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +MRID 555555 +DFOP + +χ +2 + +error level += +5.25% + + + + + + + + + + + + + + + + +0 +100 +200 +300 +400 + + + + +-10 +0 +10 + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +DFOP residuals + + + + + + diff --git a/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg b/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg deleted file mode 100644 index 58f57e93..00000000 --- a/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg +++ /dev/null @@ -1,450 +0,0 @@ - - - - - - - - - - - -0 -100 -200 -300 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -MRID 555555 -SFO - -χ -2 - -error level -= -9.04% - - - - - - - - - - - - - - - - -0 -100 -200 -300 -400 - - - - - - --20 --10 -0 -10 -20 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SFO residuals - - - - - - - - - - - - - - - -0 -100 -200 -300 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -MRID 555555 -IORE - -χ -2 - -error level -= -5.65% - - - - - - - - - - - - - - - - -0 -100 -200 -300 -400 - - - - - - --20 --10 -0 -10 -20 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -IORE residuals - - - - - - - - - - - - - - - -0 -100 -200 -300 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -MRID 555555 -DFOP - -χ -2 - -error level -= -5.25% - - - - - - - - - - - - - - - - -0 -100 -200 -300 -400 - - - - --10 -0 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -DFOP residuals - - - - - - diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index 3615c278..10de3ce0 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -16,7 +16,7 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see -context("Evaluations according to the NAFTA guidance from 2015") +context("Evaluations according to 2015 NAFTA guidance") test_that("Data for more than one compound are rejected", expect_error(nafta(FOCUS_2006_D))) @@ -40,5 +40,5 @@ test_that("Test data from Appendix D are correctly evaluated", { expect_known_output(print(res), "print_nafta_analysis.txt") plot_nafta <- function() plot(res) - vdiffr::expect_doppelganger("Plot NAFTA analysis SOP Appendix D", plot_nafta) + vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta) }) -- cgit v1.2.1