diff options
| -rw-r--r-- | log/build.log | 3 | ||||
| -rw-r--r-- | log/test.log | 83 | ||||
| -rw-r--r-- | tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 43 | ||||
| -rw-r--r-- | tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg | 1086 | ||||
| -rw-r--r-- | tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 166 | ||||
| -rw-r--r-- | tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg | 20 | ||||
| -rw-r--r-- | 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 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