From 144aed3d7b4e2c1a8c25a1a0309c1774861997a5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 23 Jul 2021 14:17:03 +0200 Subject: Fix travis config to use up to date versions of nlme, covr and devtools --- .travis.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.travis.yml b/.travis.yml index 282f1302..b1210c6a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,6 +11,10 @@ addons: cache: packages repos: CRAN: https://cloud.r-project.org +r_packages: + - nlme + - devtools + - covr r_github_packages: - saemixdevelopment/saemixextension@master script: -- cgit v1.2.1 From 24c504bb5d4d202661de5e36e6d80f2b8e906ff8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 23 Jul 2021 15:33:56 +0200 Subject: Update vdiffr tests for version 1.0 --- tests/figs/deps.txt | 3 - .../plot-errmod-with-sfo-lin-a.svg | 237 -- .../nafta-sop-appendix-b.svg | 462 ---- .../plot-nafta-analysis.svg | 450 ---- .../plotting/mixed-model-fit-for-mmkin-object.svg | 718 ------ .../plotting/mixed-model-fit-for-nlme-object.svg | 1356 ----------- ...t-for-saem-object-with-mkin-transformations.svg | 2482 -------------------- ...for-saem-object-with-saemix-transformations.svg | 713 ------ .../figs/plotting/mkinerrplot-for-focus-c-sfo.svg | 58 - .../mkinfit-plot-for-focus-c-with-defaults.svg | 63 - ...ot-for-focus-c-with-residuals-like-in-gmkin.svg | 132 -- .../mkinfit-plot-for-focus-c-with-sep-true.svg | 143 -- .../figs/plotting/mkinparplot-for-focus-c-sfo.svg | 85 - tests/figs/plotting/mmkin-plot-for-focus-c.svg | 569 ----- .../plotting/mmkin-plot-for-sfo-focus-c-and-d.svg | 300 --- tests/figs/plotting/plot-err-for-focus-d.svg | 200 -- .../figs/plotting/plot-errmod-with-focus-c-tc.svg | 128 - .../plot-errmod-with-focus-d-obs-eigen.svg | 201 -- .../plotting/plot-errmod-with-sfo-lin-a-obs.svg | 237 -- .../plotting/plot-errmod-with-sfo-lin-a-tc.svg | 235 -- tests/figs/plotting/plot-res-for-focus-c.svg | 132 -- tests/figs/plotting/plot-res-for-focus-d.svg | 196 -- .../testthat/_snaps/nafta/nafta-sop-appendix-b.svg | 447 ++++ .../testthat/_snaps/nafta/plot-nafta-analysis.svg | 435 ++++ .../plot/mixed-model-fit-for-mmkin-object.svg | 721 ++++++ .../plot/mixed-model-fit-for-nlme-object.svg | 1363 +++++++++++ .../_snaps/plot/mkinerrplot-for-focus-c-sfo.svg | 67 + .../mkinfit-plot-for-focus-c-with-defaults.svg | 72 + ...ot-for-focus-c-with-residuals-like-in-gmkin.svg | 143 ++ .../mkinfit-plot-for-focus-c-with-sep-true.svg | 151 ++ .../_snaps/plot/mkinparplot-for-focus-c-sfo.svg | 96 + .../_snaps/plot/mmkin-plot-for-focus-c.svg | 544 +++++ .../plot/mmkin-plot-for-sfo-focus-c-and-d.svg | 295 +++ .../testthat/_snaps/plot/plot-err-for-focus-d.svg | 211 ++ .../_snaps/plot/plot-errmod-with-focus-c-tc.svg | 139 ++ .../plot/plot-errmod-with-focus-d-obs-eigen.svg | 212 ++ .../testthat/_snaps/plot/plot-res-for-focus-c.svg | 143 ++ .../testthat/_snaps/plot/plot-res-for-focus-d.svg | 207 ++ tests/testthat/test_nafta.R | 10 +- tests/testthat/test_plot.R | 2 - 40 files changed, 5248 insertions(+), 9110 deletions(-) delete mode 100644 tests/figs/deps.txt delete mode 100644 tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg delete mode 100644 tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg delete mode 100644 tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg delete mode 100644 tests/figs/plotting/mixed-model-fit-for-mmkin-object.svg delete mode 100644 tests/figs/plotting/mixed-model-fit-for-nlme-object.svg delete mode 100644 tests/figs/plotting/mixed-model-fit-for-saem-object-with-mkin-transformations.svg delete mode 100644 tests/figs/plotting/mixed-model-fit-for-saem-object-with-saemix-transformations.svg delete mode 100644 tests/figs/plotting/mkinerrplot-for-focus-c-sfo.svg delete mode 100644 tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg delete mode 100644 tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg delete mode 100644 tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg delete mode 100644 tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg delete mode 100644 tests/figs/plotting/mmkin-plot-for-focus-c.svg delete mode 100644 tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg delete mode 100644 tests/figs/plotting/plot-err-for-focus-d.svg delete mode 100644 tests/figs/plotting/plot-errmod-with-focus-c-tc.svg delete mode 100644 tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg delete mode 100644 tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg delete mode 100644 tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg delete mode 100644 tests/figs/plotting/plot-res-for-focus-c.svg delete mode 100644 tests/figs/plotting/plot-res-for-focus-d.svg create mode 100644 tests/testthat/_snaps/nafta/nafta-sop-appendix-b.svg create mode 100644 tests/testthat/_snaps/nafta/plot-nafta-analysis.svg create mode 100644 tests/testthat/_snaps/plot/mixed-model-fit-for-mmkin-object.svg create mode 100644 tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg create mode 100644 tests/testthat/_snaps/plot/mkinerrplot-for-focus-c-sfo.svg create mode 100644 tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-defaults.svg create mode 100644 tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg create mode 100644 tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-sep-true.svg create mode 100644 tests/testthat/_snaps/plot/mkinparplot-for-focus-c-sfo.svg create mode 100644 tests/testthat/_snaps/plot/mmkin-plot-for-focus-c.svg create mode 100644 tests/testthat/_snaps/plot/mmkin-plot-for-sfo-focus-c-and-d.svg create mode 100644 tests/testthat/_snaps/plot/plot-err-for-focus-d.svg create mode 100644 tests/testthat/_snaps/plot/plot-errmod-with-focus-c-tc.svg create mode 100644 tests/testthat/_snaps/plot/plot-errmod-with-focus-d-obs-eigen.svg create mode 100644 tests/testthat/_snaps/plot/plot-res-for-focus-c.svg create mode 100644 tests/testthat/_snaps/plot/plot-res-for-focus-d.svg diff --git a/tests/figs/deps.txt b/tests/figs/deps.txt deleted file mode 100644 index 1fcd9257..00000000 --- a/tests/figs/deps.txt +++ /dev/null @@ -1,3 +0,0 @@ -- vdiffr-svg-engine: 1.0 -- vdiffr: 0.3.3 -- freetypeharfbuzz: 0.2.6 diff --git a/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg b/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg deleted file mode 100644 index 88e7aaee..00000000 --- a/tests/figs/error-model-fitting/plot-errmod-with-sfo-lin-a.svg +++ /dev/null @@ -1,237 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -M1 -M2 - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - - - -0 -5 -10 -15 -20 -25 -30 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg b/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg deleted file mode 100644 index d63d8da2..00000000 --- a/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg +++ /dev/null @@ -1,462 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -10 -20 -30 -40 -50 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - -aerobic aquatic -SFO - -χ -2 - -error level -= -20.4% - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 -140 - - - - --5 -0 -5 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - -SFO residuals - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -10 -20 -30 -40 -50 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - -aerobic aquatic -IORE - -χ -2 - -error level -= -5.06% - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 -140 - - - - --2 -0 -2 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - -IORE residuals - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -10 -20 -30 -40 -50 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - -aerobic aquatic -DFOP - -χ -2 - -error level -= -3.39% - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 -140 - - - - - - - - --3 --2 --1 -0 -1 -2 -3 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - -DFOP residuals - - - - - - 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 deleted file mode 100644 index 283c5c9e..00000000 --- a/tests/figs/evaluations-according-to-2015-nafta-guidance/plot-nafta-analysis.svg +++ /dev/null @@ -1,450 +0,0 @@ - - - - - - - - - - - -0 -100 -200 -300 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -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 -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -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 -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -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/plotting/mixed-model-fit-for-mmkin-object.svg b/tests/figs/plotting/mixed-model-fit-for-mmkin-object.svg deleted file mode 100644 index b3abac39..00000000 --- a/tests/figs/plotting/mixed-model-fit-for-mmkin-object.svg +++ /dev/null @@ -1,718 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -Population -Dataset 6 -Dataset 7 -Dataset 8 -Dataset 9 -Dataset 10 - - - - - - - - - - - - - - - - -0 -50 -100 -150 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residues parent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -50 -100 -150 - - - - - - - -0 -5 -10 -15 -20 -25 - - - - - - -Time -Residues A1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -5 -10 -15 -20 -25 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mixed-model-fit-for-nlme-object.svg b/tests/figs/plotting/mixed-model-fit-for-nlme-object.svg deleted file mode 100644 index 3eb2b0f8..00000000 --- a/tests/figs/plotting/mixed-model-fit-for-nlme-object.svg +++ /dev/null @@ -1,1356 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Population -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 -11 -12 -13 -14 -15 - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residues parent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/figs/plotting/mixed-model-fit-for-saem-object-with-mkin-transformations.svg deleted file mode 100644 index ce93625d..00000000 --- a/tests/figs/plotting/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ /dev/null @@ -1,2482 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Population -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 -11 -12 -13 -14 -15 - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -parent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -10 -20 -30 -40 - - - - - - -Time -m1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -10 -20 -30 -40 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mixed-model-fit-for-saem-object-with-saemix-transformations.svg b/tests/figs/plotting/mixed-model-fit-for-saem-object-with-saemix-transformations.svg deleted file mode 100644 index e6bee1c5..00000000 --- a/tests/figs/plotting/mixed-model-fit-for-saem-object-with-saemix-transformations.svg +++ /dev/null @@ -1,713 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - -Population -Dataset 6 -Dataset 7 -Dataset 8 -Dataset 9 -Dataset 10 - - - - - - - - - - - - - - - - -0 -50 -100 -150 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -parent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -50 -100 -150 - - - - - - - -0 -5 -10 -15 -20 -25 - - - - - - -Time -A1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0 -5 -10 -15 -20 -25 - - - - - - --4 --2 -0 -2 -4 - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mkinerrplot-for-focus-c-sfo.svg b/tests/figs/plotting/mkinerrplot-for-focus-c-sfo.svg deleted file mode 100644 index 186d4aac..00000000 --- a/tests/figs/plotting/mkinerrplot-for-focus-c-sfo.svg +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - -0 -20 -40 -60 -80 - - - - - - -0 -20 -40 -60 -80 - -Predicted -Squared residual - - - - - - - - - - - - - - - - - -parent - diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg deleted file mode 100644 index ef238a51..00000000 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-defaults.svg +++ /dev/null @@ -1,63 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg deleted file mode 100644 index bef1556f..00000000 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg deleted file mode 100644 index 54f0e961..00000000 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg +++ /dev/null @@ -1,143 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - -χ -2 - -error level -= -15.8% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg deleted file mode 100644 index 62590397..00000000 --- a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg +++ /dev/null @@ -1,85 +0,0 @@ - - - - - - - - - - - - - -0 -20 -40 -60 -80 - - - - - - - - - - - -parent_0 - - - - - - - - - - - - - - - - - - - - -0.0 -0.1 -0.2 -0.3 -0.4 - - - - - - - - - - - - -k_parent - - - - - - - - - diff --git a/tests/figs/plotting/mmkin-plot-for-focus-c.svg b/tests/figs/plotting/mmkin-plot-for-focus-c.svg deleted file mode 100644 index 0f824e6c..00000000 --- a/tests/figs/plotting/mmkin-plot-for-focus-c.svg +++ /dev/null @@ -1,569 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - -FOCUS_C -SFO - -χ -2 - -error level -= -15.8% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - -SFO residuals - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - -FOCUS_C -FOMC - -χ -2 - -error level -= -6.66% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - - --3 --1 -1 -2 -3 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - -FOMC residuals - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - -FOCUS_C -DFOP - -χ -2 - -error level -= -2.66% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - - --1.5 --0.5 -0.5 -1.5 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - -DFOP residuals - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - -FOCUS_C -HS - -χ -2 - -error level -= -4.7% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --2 --1 -0 -1 -2 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - -HS residuals - - - - - - diff --git a/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg b/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg deleted file mode 100644 index 40aa6bef..00000000 --- a/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - -SFO -FOCUS_C - -χ -2 - -error level -= -15.8% - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - -FOCUS_C residuals - - - - - - - - - - - - - - - -0 -20 -40 -60 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SFO -FOCUS_D - -χ -2 - -error level -= -6.45% - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -FOCUS_D residuals - - - - - - diff --git a/tests/figs/plotting/plot-err-for-focus-d.svg b/tests/figs/plotting/plot-err-for-focus-d.svg deleted file mode 100644 index 53049f6e..00000000 --- a/tests/figs/plotting/plot-err-for-focus-d.svg +++ /dev/null @@ -1,200 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -m1 - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 -140 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg b/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg deleted file mode 100644 index b0d84808..00000000 --- a/tests/figs/plotting/plot-errmod-with-focus-c-tc.svg +++ /dev/null @@ -1,128 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg b/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg deleted file mode 100644 index d5e1b6b2..00000000 --- a/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -m1 - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 -140 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg deleted file mode 100644 index 42fbdc84..00000000 --- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg +++ /dev/null @@ -1,237 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -M1 -M2 - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - - - -0 -5 -10 -15 -20 -25 -30 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg deleted file mode 100644 index f4e7679d..00000000 --- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Observed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -M1 -M2 - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - - - -0 -5 -10 -15 -20 -25 -30 - - - - - - -Predicted -Squared residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-res-for-focus-c.svg b/tests/figs/plotting/plot-res-for-focus-c.svg deleted file mode 100644 index 3e6de1ce..00000000 --- a/tests/figs/plotting/plot-res-for-focus-c.svg +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - -0 -20 -40 -60 -80 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - -parent - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/figs/plotting/plot-res-for-focus-d.svg b/tests/figs/plotting/plot-res-for-focus-d.svg deleted file mode 100644 index 222d85f6..00000000 --- a/tests/figs/plotting/plot-res-for-focus-d.svg +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - - -0 -20 -40 -60 -80 -100 - - - - - - -Time -Residue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent -m1 - - - - - - - - - - - - - - - - - - -0 -20 -40 -60 -80 -100 -120 - - - - - - --10 --5 -0 -5 -10 - - - - - - -Time -Residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/_snaps/nafta/nafta-sop-appendix-b.svg b/tests/testthat/_snaps/nafta/nafta-sop-appendix-b.svg new file mode 100644 index 00000000..92d77fbe --- /dev/null +++ b/tests/testthat/_snaps/nafta/nafta-sop-appendix-b.svg @@ -0,0 +1,447 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +10 +20 +30 +40 +50 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + + +aerobic aquatic +SFO + +χ +2 + +error level += +20.4% + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 +140 + + + + +-5 +0 +5 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + +SFO residuals + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +10 +20 +30 +40 +50 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + +aerobic aquatic +IORE + +χ +2 + +error level += +5.06% + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 +140 + + + + +-2 +0 +2 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + +IORE residuals + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +10 +20 +30 +40 +50 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + +aerobic aquatic +DFOP + +χ +2 + +error level += +3.39% + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 +140 + + + + + + + + +-3 +-2 +-1 +0 +1 +2 +3 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + +DFOP residuals + + + + + + + + + diff --git a/tests/testthat/_snaps/nafta/plot-nafta-analysis.svg b/tests/testthat/_snaps/nafta/plot-nafta-analysis.svg new file mode 100644 index 00000000..a4198ede --- /dev/null +++ b/tests/testthat/_snaps/nafta/plot-nafta-analysis.svg @@ -0,0 +1,435 @@ + + + + + + + + + + + + + + + + + +0 +100 +200 +300 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + + + + + + +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 +Residue + + + + + + + + + + + + + + + + + + + + + + + +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 +Residue + + + + + + + + + + + + + + + + + + + + + + + +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/_snaps/plot/mixed-model-fit-for-mmkin-object.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-mmkin-object.svg new file mode 100644 index 00000000..ed0998e5 --- /dev/null +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-mmkin-object.svg @@ -0,0 +1,721 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Population +Dataset 6 +Dataset 7 +Dataset 8 +Dataset 9 +Dataset 10 + + + + + + + + + + + + + + + +0 +50 +100 +150 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residues parent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + +-4 +-2 +0 +2 +4 + + + + + + + + +Predicted +Standardized residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +50 +100 +150 + + + + + + + +0 +5 +10 +15 +20 +25 + + + + + + + + +Time +Residues A1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +5 +10 +15 +20 +25 + + + + + + +-4 +-2 +0 +2 +4 + + + + + + + + +Predicted +Standardized residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg new file mode 100644 index 00000000..a4396bff --- /dev/null +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg @@ -0,0 +1,1363 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Population +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residues parent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + +-4 +-2 +0 +2 +4 + + + + + + + + +Predicted +Standardized residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mkinerrplot-for-focus-c-sfo.svg b/tests/testthat/_snaps/plot/mkinerrplot-for-focus-c-sfo.svg new file mode 100644 index 00000000..84768b51 --- /dev/null +++ b/tests/testthat/_snaps/plot/mkinerrplot-for-focus-c-sfo.svg @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 + + + + + + +0 +20 +40 +60 +80 + +Predicted +Squared residual + + + + + + + + + + + + + + + + + + + +parent + + diff --git a/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-defaults.svg b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-defaults.svg new file mode 100644 index 00000000..dc8eb988 --- /dev/null +++ b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-defaults.svg @@ -0,0 +1,72 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + diff --git a/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg new file mode 100644 index 00000000..371dc61f --- /dev/null +++ b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-sep-true.svg b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-sep-true.svg new file mode 100644 index 00000000..e591058b --- /dev/null +++ b/tests/testthat/_snaps/plot/mkinfit-plot-for-focus-c-with-sep-true.svg @@ -0,0 +1,151 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + +χ +2 + +error level += +15.8% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mkinparplot-for-focus-c-sfo.svg b/tests/testthat/_snaps/plot/mkinparplot-for-focus-c-sfo.svg new file mode 100644 index 00000000..0b9a91b0 --- /dev/null +++ b/tests/testthat/_snaps/plot/mkinparplot-for-focus-c-sfo.svg @@ -0,0 +1,96 @@ + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 + + + + + + + + + + + + + + + +parent_0 + + + + + + + + + + + + + + + + + + + +0.0 +0.1 +0.2 +0.3 +0.4 + + + + + + + + + + + +k_parent + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mmkin-plot-for-focus-c.svg b/tests/testthat/_snaps/plot/mmkin-plot-for-focus-c.svg new file mode 100644 index 00000000..50ea8054 --- /dev/null +++ b/tests/testthat/_snaps/plot/mmkin-plot-for-focus-c.svg @@ -0,0 +1,544 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + +FOCUS_C +SFO + +χ +2 + +error level += +15.8% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + +SFO residuals + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + +FOCUS_C +FOMC + +χ +2 + +error level += +6.66% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + + +-3 +-1 +1 +2 +3 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + +FOMC residuals + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + +FOCUS_C +DFOP + +χ +2 + +error level += +2.66% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + + +-1.5 +-0.5 +0.5 +1.5 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + +DFOP residuals + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + +FOCUS_C +HS + +χ +2 + +error level += +4.7% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-2 +-1 +0 +1 +2 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + +HS residuals + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mmkin-plot-for-sfo-focus-c-and-d.svg b/tests/testthat/_snaps/plot/mmkin-plot-for-sfo-focus-c-and-d.svg new file mode 100644 index 00000000..29d20bcf --- /dev/null +++ b/tests/testthat/_snaps/plot/mmkin-plot-for-sfo-focus-c-and-d.svg @@ -0,0 +1,295 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + +SFO +FOCUS_C + +χ +2 + +error level += +15.8% + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + +FOCUS_C residuals + + + + + + + + + + + + + + +0 +20 +40 +60 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + +SFO +FOCUS_D + +χ +2 + +error level += +6.45% + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + + + +FOCUS_D residuals + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/plot-err-for-focus-d.svg b/tests/testthat/_snaps/plot/plot-err-for-focus-d.svg new file mode 100644 index 00000000..249f53ed --- /dev/null +++ b/tests/testthat/_snaps/plot/plot-err-for-focus-d.svg @@ -0,0 +1,211 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +parent +m1 + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 +140 + + + + + + + + +Predicted +Squared residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/plot-errmod-with-focus-c-tc.svg b/tests/testthat/_snaps/plot/plot-errmod-with-focus-c-tc.svg new file mode 100644 index 00000000..0d43eb9b --- /dev/null +++ b/tests/testthat/_snaps/plot/plot-errmod-with-focus-c-tc.svg @@ -0,0 +1,139 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Predicted +Squared residual + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/plot-errmod-with-focus-d-obs-eigen.svg b/tests/testthat/_snaps/plot/plot-errmod-with-focus-d-obs-eigen.svg new file mode 100644 index 00000000..0a0f1ed5 --- /dev/null +++ b/tests/testthat/_snaps/plot/plot-errmod-with-focus-d-obs-eigen.svg @@ -0,0 +1,212 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +parent +m1 + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 +140 + + + + + + + + +Predicted +Squared residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/plot-res-for-focus-c.svg b/tests/testthat/_snaps/plot/plot-res-for-focus-c.svg new file mode 100644 index 00000000..05699fae --- /dev/null +++ b/tests/testthat/_snaps/plot/plot-res-for-focus-c.svg @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +0 +20 +40 +60 +80 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + +parent + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/plot-res-for-focus-d.svg b/tests/testthat/_snaps/plot/plot-res-for-focus-d.svg new file mode 100644 index 00000000..b735f33e --- /dev/null +++ b/tests/testthat/_snaps/plot/plot-res-for-focus-d.svg @@ -0,0 +1,207 @@ + + + + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residue + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +parent +m1 + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + +-10 +-5 +0 +5 +10 + + + + + + + + +Time +Residual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index 80b6adba..8eb052c5 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -21,10 +21,7 @@ test_that("Test data from Appendix B are correctly evaluated", { expect_known_output(print(res), "NAFTA_SOP_Appendix_B.txt") plot_nafta <- function() plot(res) - if(requireNamespace("vdiffr", quietly = TRUE)) { - skip_if(getRversion() >= "4.1.0") - vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta) - } + vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta) }) test_that("Test data from Appendix D are correctly evaluated", { @@ -49,8 +46,5 @@ test_that("Test data from Appendix D are correctly evaluated", { expect_known_output(print(res), "NAFTA_SOP_Appendix_D.txt") plot_nafta <- function() plot(res) - if(requireNamespace("vdiffr", quietly = TRUE)) { - skip_if(getRversion() >= "4.1.0") - vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta) - } + vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta) }) diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 0bf3ee66..28c537bb 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -14,8 +14,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { fit_C_tc <- mkinfit("SFO", FOCUS_2006_C, error_model = "tc", quiet = TRUE) plot_errmod_fit_C_tc <- function() plot_err(fit_C_tc) - - skip_if(getRversion() >= "4.1.0") vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with defaults", plot_default_FOCUS_C_SFO) vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with residuals like in gmkin", plot_res_FOCUS_C_SFO) vdiffr::expect_doppelganger("plot_res for FOCUS C", plot_res_FOCUS_C_SFO_2) -- cgit v1.2.1 From 297285ac86a74c1ceb517aac9eca46d07513c45d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 23 Jul 2021 15:43:02 +0200 Subject: Rerun tests, use current vdiffr on travis --- .travis.yml | 1 + GNUmakefile | 3 -- test.log | 42 ++++++------------------ vignettes/FOCUS_D.html | 14 ++++---- vignettes/mkin.html | 88 +++++++++++++++++++++++--------------------------- vignettes/twa.html | 2 +- 6 files changed, 58 insertions(+), 92 deletions(-) diff --git a/.travis.yml b/.travis.yml index b1210c6a..e64c9dca 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,6 +15,7 @@ r_packages: - nlme - devtools - covr + - vdiffr r_github_packages: - saemixdevelopment/saemixextension@master script: diff --git a/GNUmakefile b/GNUmakefile index 8604d3b3..a6abacac 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -90,9 +90,6 @@ slowtests: install NOT_CRAN=true "$(RBIN)/Rscript" -e 'library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log sed -i -e "s/\r.*\r//" tests_slow.log -vdiffr: - "$(RBIN)/Rscript" -e 'vdiffr::manage_cases(filter = "plot|nafta")' - testcheck: roxygen test check README.html: README.md diff --git a/test.log b/test.log index a8b42364..1f477869 100644 --- a/test.log +++ b/test.log @@ -3,11 +3,11 @@ Loading required package: parallel ℹ Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2 s] +✔ | 5 | Analytical solutions for coupled models [3.1 s] ✔ | 5 | Calculation of Akaike weights ✔ | 2 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.3 s] -✔ | 14 | Error model fitting [4.3 s] +✔ | 14 | Error model fitting [4.2 s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7 s] @@ -19,43 +19,19 @@ Loading required package: parallel ✔ | 1 | mkinfit features [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s] -✖ | 7 1 | Nonlinear mixed-effects models [1.9 s] -──────────────────────────────────────────────────────────────────────────────── -Error (test_nlme.R:116:3): nlme_function works correctly in other cases -Error: unused argument ("sysname") -Backtrace: - 1. mkin::mmkin("SFO", ds_me_sfo_5, quiet = TRUE) test_nlme.R:116:2 - 2. parallel::mclapply(...) /home/jranke/git/mkin/R/mmkin.R:118:4 -──────────────────────────────────────────────────────────────────────────────── -✖ | 10 4 | Plotting [1.7 s] -──────────────────────────────────────────────────────────────────────────────── -Failure (test_plot.R:20:3): Plotting mkinfit, mmkin and mixed model objects is reproducible -Figures don't match: mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg - - -Failure (test_plot.R:21:3): Plotting mkinfit, mmkin and mixed model objects is reproducible -Figures don't match: plot-res-for-focus-c.svg - - -Failure (test_plot.R:22:3): Plotting mkinfit, mmkin and mixed model objects is reproducible -Figures don't match: mkinfit-plot-for-focus-c-with-sep-true.svg - - -Failure (test_plot.R:30:3): Plotting mkinfit, mmkin and mixed model objects is reproducible -Figures don't match: plot-res-for-focus-d.svg - -──────────────────────────────────────────────────────────────────────────────── +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s] +✔ | 9 | Nonlinear mixed-effects models [7.9 s] +✔ | 14 | Plotting [1.1 s] ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] -✔ | 7 | Fitting the SFORB model [3.6 s] +✔ | 7 | Fitting the SFORB model [3.7 s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Summary [0.1 s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] -✔ | 9 | Hypothesis tests [8.1 s] +✔ | 9 | Hypothesis tests [8.0 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 35.2 s +Duration: 40.3 s -[ FAIL 5 | WARN 0 | SKIP 0 | PASS 168 ] +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ] diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index f740cfc0..c2599ee5 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -363,7 +363,7 @@ pre code {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

Last change 31 January 2019 (rebuilt 2021-03-31)

+

Last change 31 January 2019 (rebuilt 2021-07-23)

@@ -431,16 +431,16 @@ print(FOCUS_2006_D) ## of zero were removed from the data

A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

plot_sep(fit, lpos = c("topright", "bottomright"))
-

+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    1.0.4 
-## R version used for fitting:       4.0.4 
-## Date of fit:     Wed Mar 31 19:01:35 2021 
-## Date of summary: Wed Mar 31 19:01:35 2021 
+
## mkin version used for fitting:    1.1.0 
+## R version used for fitting:       4.1.0 
+## Date of fit:     Fri Jul 23 15:39:43 2021 
+## Date of summary: Fri Jul 23 15:39:43 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -448,7 +448,7 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.146 s
+## Fitted using 401 model solutions performed in 0.152 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/vignettes/mkin.html b/vignettes/mkin.html
index 3a49375a..4afe6afd 100644
--- a/vignettes/mkin.html
+++ b/vignettes/mkin.html
@@ -60,6 +60,15 @@ if (!!window.navigator.userAgent.match("MSIE 8")) {
 !function(a){"use strict";a.matchMedia=a.matchMedia||function(a){var b,c=a.documentElement,d=c.firstElementChild||c.firstChild,e=a.createElement("body"),f=a.createElement("div");return f.id="mq-test-1",f.style.cssText="position:absolute;top:-100em",e.style.background="none",e.appendChild(f),function(a){return f.innerHTML='­',c.insertBefore(e,d),b=42===f.offsetWidth,c.removeChild(e),{matches:b,media:a}}}(a.document)}(this),function(a){"use strict";function b(){u(!0)}var c={};a.respond=c,c.update=function(){};var d=[],e=function(){var b=!1;try{b=new a.XMLHttpRequest}catch(c){b=new a.ActiveXObject("Microsoft.XMLHTTP")}return function(){return b}}(),f=function(a,b){var c=e();c&&(c.open("GET",a,!0),c.onreadystatechange=function(){4!==c.readyState||200!==c.status&&304!==c.status||b(c.responseText)},4!==c.readyState&&c.send(null))};if(c.ajax=f,c.queue=d,c.regex={media:/@media[^\{]+\{([^\{\}]*\{[^\}\{]*\})+/gi,keyframes:/@(?:\-(?:o|moz|webkit)\-)?keyframes[^\{]+\{(?:[^\{\}]*\{[^\}\{]*\})+[^\}]*\}/gi,urls:/(url\()['"]?([^\/\)'"][^:\)'"]+)['"]?(\))/g,findStyles:/@media *([^\{]+)\{([\S\s]+?)$/,only:/(only\s+)?([a-zA-Z]+)\s?/,minw:/\([\s]*min\-width\s*:[\s]*([\s]*[0-9\.]+)(px|em)[\s]*\)/,maxw:/\([\s]*max\-width\s*:[\s]*([\s]*[0-9\.]+)(px|em)[\s]*\)/},c.mediaQueriesSupported=a.matchMedia&&null!==a.matchMedia("only all")&&a.matchMedia("only all").matches,!c.mediaQueriesSupported){var g,h,i,j=a.document,k=j.documentElement,l=[],m=[],n=[],o={},p=30,q=j.getElementsByTagName("head")[0]||k,r=j.getElementsByTagName("base")[0],s=q.getElementsByTagName("link"),t=function(){var a,b=j.createElement("div"),c=j.body,d=k.style.fontSize,e=c&&c.style.fontSize,f=!1;return b.style.cssText="position:absolute;font-size:1em;width:1em",c||(c=f=j.createElement("body"),c.style.background="none"),k.style.fontSize="100%",c.style.fontSize="100%",c.appendChild(b),f&&k.insertBefore(c,k.firstChild),a=b.offsetWidth,f?k.removeChild(c):c.removeChild(b),k.style.fontSize=d,e&&(c.style.fontSize=e),a=i=parseFloat(a)},u=function(b){var c="clientWidth",d=k[c],e="CSS1Compat"===j.compatMode&&d||j.body[c]||d,f={},o=s[s.length-1],r=(new Date).getTime();if(b&&g&&p>r-g)return a.clearTimeout(h),h=a.setTimeout(u,p),void 0;g=r;for(var v in l)if(l.hasOwnProperty(v)){var w=l[v],x=w.minw,y=w.maxw,z=null===x,A=null===y,B="em";x&&(x=parseFloat(x)*(x.indexOf(B)>-1?i||t():1)),y&&(y=parseFloat(y)*(y.indexOf(B)>-1?i||t():1)),w.hasquery&&(z&&A||!(z||e>=x)||!(A||y>=e))||(f[w.media]||(f[w.media]=[]),f[w.media].push(m[w.rules]))}for(var C in n)n.hasOwnProperty(C)&&n[C]&&n[C].parentNode===q&&q.removeChild(n[C]);n.length=0;for(var D in f)if(f.hasOwnProperty(D)){var E=j.createElement("style"),F=f[D].join("\n");E.type="text/css",E.media=D,q.insertBefore(E,o.nextSibling),E.styleSheet?E.styleSheet.cssText=F:E.appendChild(j.createTextNode(F)),n.push(E)}},v=function(a,b,d){var e=a.replace(c.regex.keyframes,"").match(c.regex.media),f=e&&e.length||0;b=b.substring(0,b.lastIndexOf("/"));var g=function(a){return a.replace(c.regex.urls,"$1"+b+"$2$3")},h=!f&&d;b.length&&(b+="/"),h&&(f=1);for(var i=0;f>i;i++){var j,k,n,o;h?(j=d,m.push(g(a))):(j=e[i].match(c.regex.findStyles)&&RegExp.$1,m.push(RegExp.$2&&g(RegExp.$2))),n=j.split(","),o=n.length;for(var p=0;o>p;p++)k=n[p],l.push({media:k.split("(")[0].match(c.regex.only)&&RegExp.$2||"all",rules:m.length-1,hasquery:k.indexOf("(")>-1,minw:k.match(c.regex.minw)&&parseFloat(RegExp.$1)+(RegExp.$2||""),maxw:k.match(c.regex.maxw)&&parseFloat(RegExp.$1)+(RegExp.$2||"")})}u()},w=function(){if(d.length){var b=d.shift();f(b.href,function(c){v(c,b.href,b.media),o[b.href]=!0,a.setTimeout(function(){w()},0)})}},x=function(){for(var b=0;b
+
 
@@ -1776,6 +1765,9 @@ $(document).ready(function () {