From 448e47e756c0c67fc658f93575092973aa455fb1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 08:53:15 +0200 Subject: Point to the dmta pathway vignette in the dmta test --- tests/testthat/test_dmta.R | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R index cd6de341..3941cae1 100644 --- a/tests/testthat/test_dmta.R +++ b/tests/testthat/test_dmta.R @@ -85,9 +85,12 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid "Iteration 5, LME step.*not converge") ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed") - skip("Fitting this ODE model with saemix takes about 15 minutes on my system") + skip("Fitting this ODE model with saemix takes about 5 minutes on my new system") + # August 2023: Please refer to the mkin vignette for the currently + # recommended way to fit the DMTA pathway data with saemix + # As DFOP is overparameterised and leads to instabilities and errors, we - # need to use SFO. + # need to use SFO with nlme # saem_saemix_sfo_sfo3p_tc <- saem(dmta_sfo_sfo3p_tc) # The fit above, using SFO for the parent leads to low values of DMTA_0 # (confidence interval from 84.4 to 92.8) which is not consistent with what -- cgit v1.2.1 From 9901675e499226eec6304113eb5ffa3b900942c2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:03:53 +0200 Subject: Update platform specific tests on desktop --- log/build.log | 3 + log/test.log | 114 +- .../_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 43 +- ...t-for-saem-object-with-mkin-transformations.svg | 1086 ++++++++++---------- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 166 +-- .../plot/mixed-model-fit-for-nlme-object.svg | 20 +- tests/testthat/print_dfop_saem_1.txt | 10 +- 7 files changed, 746 insertions(+), 696 deletions(-) diff --git a/log/build.log b/log/build.log index 717128fd..01173753 100644 --- a/log/build.log +++ b/log/build.log @@ -7,4 +7,7 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/vignettes/web_only’ * building ‘mkin_1.2.5.tar.gz’ +Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : + storing paths of more than 100 bytes is not portable: + ‘mkin/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.new.svg’ diff --git a/log/test.log b/log/test.log index c872cb1d..72234347 100644 --- a/log/test.log +++ b/log/test.log @@ -1,50 +1,96 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.1s] +✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [5.3s] -✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [31.5s] -✔ | 14 | Error model fitting [5.6s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] +✔ | 12 | Confidence intervals and p-values [0.4s] +✔ | 1 12 | Dimethenamid data from 2018 [12.9s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system +──────────────────────────────────────────────────────────────────────────────── +✔ | 14 | Error model fitting [2.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) -✔ | 4 | Test fitting the decline of metabolites from their maximum -✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.1s] -✔ | 2 16 | Nonlinear mixed-effects models [441.3s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] +✔ | 1 | Fitting the logistic model [0.1s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] +✔ | 2 16 | Nonlinear mixed-effects models [148.3s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits +Reason: Fitting with saemix takes around 10 minutes when using deSolve + +Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work +Reason: This is seldom used, so save some time +──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls -✔ | 3 | mkinfit features +✔ | 10 | Special cases of mkinfit calls [0.3s] +✔ | 3 | mkinfit features [0.5s] ✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [71.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] -✔ | 9 | Nonlinear mixed-effects models with nlme [10.1s] -✔ | 15 | Plotting [12.1s] +✔ | 3 | Model predictions with mkinpredict [0.1s] +✖ | 3 9 | Multistart method for saem.mmkin models [22.9s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger(...) + at test_multistart.R:44:2 + 3. testthat::expect_snapshot_file(...) + +Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) + at test_multistart.R:55:2 + 3. testthat::expect_snapshot_file(...) + +Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) + at test_multistart.R:56:2 + 3. testthat::expect_snapshot_file(...) +──────────────────────────────────────────────────────────────────────────────── +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✖ | 1 14 | Plotting [4.6s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_plot.R:55:3'): Plotting mkinfit, mmkin and mixed model objects is reproducible +Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed +Run `testthat::snapshot_review('plot/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger(...) + at test_plot.R:55:2 + 3. testthat::expect_snapshot_file(...) +──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [81.8s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] +✔ | 1 36 | saemix parent models [31.2s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem +Reason: This still takes almost 2.5 minutes although we do not solve ODEs +──────────────────────────────────────────────────────────────────────────────── +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] -✔ | 9 | Hypothesis tests [7.3s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.5s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 9 | Hypothesis tests [2.9s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 731.0 s +Duration: 260.5 s -── Skipped tests (4) ─────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 15 minutes on my system (1): - 'test_dmta.R:88:3' -• Fitting with saemix takes around 10 minutes when using deSolve (1): - 'test_mixed.R:80:3' -• This is seldom used, so save some time (1): 'test_mixed.R:133:3' -• This still takes almost 2.5 minutes although we do not solve ODEs (1): - 'test_saemix_parent.R:143:3' +── Skipped tests ────────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 5 minutes on my new system (1) +• Fitting with saemix takes around 10 minutes when using deSolve (1) +• This is seldom used, so save some time (1) +• This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] +[ FAIL 4 | WARN 0 | SKIP 4 | PASS 277 ] diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg index 3b9d51fb..6015aed8 100644 --- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg @@ -21,26 +21,28 @@ Frequency of log likelihoods - - - - - + + + + --1149.30 --1149.25 --1149.20 --1149.15 --1149.10 --1149.05 --1149.00 +-1149.5 +-1149.4 +-1149.3 +-1149.2 +-1149.1 +-1149.0 + + 0 -1 -2 +1 +2 +3 +4 @@ -48,13 +50,12 @@ - - - - - - - + + + + + + original fit diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg index 5e534dd1..69fa6a4d 100644 --- a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -249,7 +249,7 @@ - + @@ -342,7 +342,7 @@ - + @@ -856,38 +856,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -933,51 +933,51 @@ - - - + + + - - + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -1502,7 +1502,7 @@ - + @@ -1585,7 +1585,7 @@ - + @@ -1940,17 +1940,17 @@ - + - - - - + + + + 0 -10 -20 -30 -40 +10 +20 +30 +40 @@ -1983,290 +1983,290 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2274,47 +2274,47 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2323,174 +2323,174 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg index ed9168fb..b01dac74 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -25,104 +25,104 @@ - - - + + + - + - - - - - + + + + + - - - - - - + + + + + + - - - + + + - - - - - - + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - + + + + - + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + - - - - - - + + + + + + - - + + - - - - - - - - - + + + + + + + + + - - + + 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 index c94012ce..76fed0dc 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg @@ -813,7 +813,7 @@ - + @@ -833,7 +833,7 @@ - + @@ -900,7 +900,7 @@ - + @@ -921,7 +921,7 @@ - + @@ -964,8 +964,8 @@ - - + + @@ -1243,8 +1243,8 @@ - - + + @@ -1291,8 +1291,8 @@ - - + + diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt index f7354320..bdc40065 100644 --- a/tests/testthat/print_dfop_saem_1.txt +++ b/tests/testthat/print_dfop_saem_1.txt @@ -13,11 +13,11 @@ Likelihood computed by importance sampling Fitted parameters: estimate lower upper -parent_0 99.96 98.82 101.11 -log_k1 -2.71 -2.94 -2.49 -log_k2 -4.14 -4.26 -4.01 -g_qlogis -0.36 -0.54 -0.17 -a.1 0.93 0.69 1.17 +parent_0 99.92 98.77 101.06 +log_k1 -2.72 -2.95 -2.50 +log_k2 -4.14 -4.27 -4.01 +g_qlogis -0.35 -0.53 -0.16 +a.1 0.92 0.68 1.16 b.1 0.05 0.04 0.06 SD.log_k1 0.37 0.23 0.51 SD.log_k2 0.23 0.14 0.31 -- cgit v1.2.1 From 49f7538f342e504d3f62faa40ca0b819ed642335 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:12:24 +0200 Subject: Update test log with libopenblas0-pthread --- log/test.log | 64 ++++++++++++++---------------------------------------------- 1 file changed, 15 insertions(+), 49 deletions(-) diff --git a/log/test.log b/log/test.log index 72234347..b36c62cd 100644 --- a/log/test.log +++ b/log/test.log @@ -1,12 +1,12 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] ✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.9s] +✔ | 1 12 | Dimethenamid data from 2018 [12.8s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system @@ -17,8 +17,8 @@ Reason: Fitting this ODE model with saemix takes about 5 minutes on my new syste ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] ✔ | 1 | Fitting the logistic model [0.1s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] -✔ | 2 16 | Nonlinear mixed-effects models [148.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.5s] +✔ | 2 16 | Nonlinear mixed-effects models [148.1s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -29,55 +29,21 @@ Reason: This is seldom used, so save some time ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.3s] ✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict [0.1s] -✖ | 3 9 | Multistart method for saem.mmkin models [22.9s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_multistart.R:44:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) - at test_multistart.R:55:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) - at test_multistart.R:56:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] -✖ | 1 14 | Plotting [4.6s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_plot.R:55:3'): Plotting mkinfit, mmkin and mixed model objects is reproducible -Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed -Run `testthat::snapshot_review('plot/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_plot.R:55:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── +✔ | 8 | mkinmod model generation and printing [0.1s] +✔ | 3 | Model predictions with mkinpredict [0.2s] +✔ | 12 | Multistart method for saem.mmkin models [28.4s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] +✔ | 15 | Plotting [4.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [31.2s] +✔ | 1 36 | saemix parent models [31.0s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] +✔ | 10 | Fitting the SFORB model [1.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] @@ -85,7 +51,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 260.5 s +Duration: 266.7 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1) @@ -93,4 +59,4 @@ Duration: 260.5 s • This is seldom used, so save some time (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 4 | WARN 0 | SKIP 4 | PASS 277 ] +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] -- cgit v1.2.1 From bbed90f6a4010ac0b911ec13c04ae06eebc74bb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:23:27 +0200 Subject: Update tests without any openblas variant This even a bit faster. --- log/build.log | 3 - log/test.log | 83 +- .../_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 43 +- ...t-for-saem-object-with-mkin-transformations.svg | 1086 ++++++++++---------- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 166 +-- .../plot/mixed-model-fit-for-nlme-object.svg | 20 +- tests/testthat/print_dfop_saem_1.txt | 10 +- 7 files changed, 731 insertions(+), 680 deletions(-) diff --git a/log/build.log b/log/build.log index 01173753..717128fd 100644 --- a/log/build.log +++ b/log/build.log @@ -7,7 +7,4 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/vignettes/web_only’ * building ‘mkin_1.2.5.tar.gz’ -Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : - storing paths of more than 100 bytes is not portable: - ‘mkin/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.new.svg’ diff --git a/log/test.log b/log/test.log index b36c62cd..6d5bc470 100644 --- a/log/test.log +++ b/log/test.log @@ -1,25 +1,46 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.6s] +✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.8s] +✔ | 1 12 | Dimethenamid data from 2018 [13.2s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [2.3s] +✔ | 14 | Error model fitting [2.5s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] ✔ | 1 | Fitting the logistic model [0.1s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.5s] -✔ | 2 16 | Nonlinear mixed-effects models [148.1s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] +✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s] ──────────────────────────────────────────────────────────────────────────────── +Failure ('test_mixed.R:21:3'): Print methods work +Results have changed from known value recorded in 'print_dfop_saem_1.txt'. + +old[13:23] vs new[13:23] + "" + "Fitted parameters:" + " estimate lower upper" +- "parent_0 99.92 98.77 101.06" ++ "parent_0 99.96 98.82 101.11" +- "log_k1 -2.72 -2.95 -2.50" ++ "log_k1 -2.71 -2.94 -2.49" +- "log_k2 -4.14 -4.27 -4.01" ++ "log_k2 -4.14 -4.26 -4.01" +- "g_qlogis -0.35 -0.53 -0.16" ++ "g_qlogis -0.36 -0.54 -0.17" +- "a.1 0.92 0.68 1.16" ++ "a.1 0.93 0.69 1.17" + "b.1 0.05 0.04 0.06" + "SD.log_k1 0.37 0.23 0.51" +and 1 more ... + Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -29,21 +50,55 @@ Reason: This is seldom used, so save some time ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.3s] ✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing [0.1s] -✔ | 3 | Model predictions with mkinpredict [0.2s] -✔ | 12 | Multistart method for saem.mmkin models [28.4s] +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict [0.1s] +✖ | 3 9 | Multistart method for saem.mmkin models [23.2s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger(...) + at test_multistart.R:44:2 + 3. testthat::expect_snapshot_file(...) + +Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) + at test_multistart.R:55:2 + 3. testthat::expect_snapshot_file(...) + +Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) + at test_multistart.R:56:2 + 3. testthat::expect_snapshot_file(...) +──────────────────────────────────────────────────────────────────────────────── ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] ✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] -✔ | 15 | Plotting [4.6s] +✖ | 1 14 | Plotting [4.7s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_plot.R:55:3'): Plotting mkinfit, mmkin and mixed model objects is reproducible +Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed +Run `testthat::snapshot_review('plot/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger(...) + at test_plot.R:55:2 + 3. testthat::expect_snapshot_file(...) +──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [31.0s] +✔ | 1 36 | saemix parent models [31.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] @@ -51,7 +106,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 266.7 s +Duration: 262.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1) @@ -59,4 +114,4 @@ Duration: 266.7 s • This is seldom used, so save some time (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] +[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ] diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg index 6015aed8..3b9d51fb 100644 --- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg @@ -21,28 +21,26 @@ Frequency of log likelihoods - - - - + + + + + --1149.5 --1149.4 --1149.3 --1149.2 --1149.1 --1149.0 +-1149.30 +-1149.25 +-1149.20 +-1149.15 +-1149.10 +-1149.05 +-1149.00 - - 0 -1 -2 -3 -4 +1 +2 @@ -50,12 +48,13 @@ - - - - - - + + + + + + + original fit diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg index 69fa6a4d..5e534dd1 100644 --- a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -249,7 +249,7 @@ - + @@ -342,7 +342,7 @@ - + @@ -856,38 +856,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -933,51 +933,51 @@ - - - + + + - - + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -1502,7 +1502,7 @@ - + @@ -1585,7 +1585,7 @@ - + @@ -1940,17 +1940,17 @@ - + - - - - + + + + 0 -10 -20 -30 -40 +10 +20 +30 +40 @@ -1983,290 +1983,290 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2274,47 +2274,47 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2323,174 +2323,174 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg index b01dac74..ed9168fb 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -25,104 +25,104 @@ - - - + + + - + - - - - - + + + + + - - - - - - + + + + + + - - - + + + - - - - - - + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - + + + + - + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + - - - - - - + + + + + + - - + + - - - - - - - - - + + + + + + + + + - - + + 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 index 76fed0dc..c94012ce 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg @@ -813,7 +813,7 @@ - + @@ -833,7 +833,7 @@ - + @@ -900,7 +900,7 @@ - + @@ -921,7 +921,7 @@ - + @@ -964,8 +964,8 @@ - - + + @@ -1243,8 +1243,8 @@ - - + + @@ -1291,8 +1291,8 @@ - - + + diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt index bdc40065..f7354320 100644 --- a/tests/testthat/print_dfop_saem_1.txt +++ b/tests/testthat/print_dfop_saem_1.txt @@ -13,11 +13,11 @@ Likelihood computed by importance sampling Fitted parameters: estimate lower upper -parent_0 99.92 98.77 101.06 -log_k1 -2.72 -2.95 -2.50 -log_k2 -4.14 -4.27 -4.01 -g_qlogis -0.35 -0.53 -0.16 -a.1 0.92 0.68 1.16 +parent_0 99.96 98.82 101.11 +log_k1 -2.71 -2.94 -2.49 +log_k2 -4.14 -4.26 -4.01 +g_qlogis -0.36 -0.54 -0.17 +a.1 0.93 0.69 1.17 b.1 0.05 0.04 0.06 SD.log_k1 0.37 0.23 0.51 SD.log_k2 0.23 0.14 0.31 -- cgit v1.2.1