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