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authorJohannes Ranke <jranke@uni-bremen.de>2022-12-07 14:41:52 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-12-07 14:41:52 +0100
commit97f71fc3d086bd447ab3e4d19abf32bb3114085b (patch)
treef5795d3f8518b8cf0f15e1ea1f04fdba81bf496a /log/test.log
parent478c6d5eec4c84b22b43adcbdf36888b302ead00 (diff)
Check slopes in saemix covariate models
Diffstat (limited to 'log/test.log')
-rw-r--r--log/test.log41
1 files changed, 16 insertions, 25 deletions
diff --git a/log/test.log b/log/test.log
index 7614b136..af2ffc41 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,23 +1,23 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.2s]
+✔ | 5 | Analytical solutions for coupled models [3.4s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.1s]
-✔ | 1 12 | Dimethenamid data from 2018 [32.0s]
+✔ | 1 12 | Dimethenamid data from 2018 [32.7s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
────────────────────────────────────────────────────────────────────────────────
-✔ | 14 | Error model fitting [4.8s]
+✔ | 14 | Error model fitting [5.0s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
✔ | 1 | Fitting the logistic model [0.2s]
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s]
-✔ | 1 11 | Nonlinear mixed-effects models [13.3s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.4s]
+✔ | 1 11 | Nonlinear mixed-effects models [13.5s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
@@ -27,40 +27,31 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.4s]
-✖ | 1 11 | Multistart method for saem.mmkin models [46.7s]
-────────────────────────────────────────────────────────────────────────────────
-Failure ('test_multistart.R:56'): 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(...)
-────────────────────────────────────────────────────────────────────────────────
+✔ | 12 | Multistart method for saem.mmkin models [50.1s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s]
-✔ | 15 | Plotting [10.1s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.8s]
+✔ | 15 | Plotting [10.5s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [73.6s]
+✔ | 1 36 | saemix parent models [85.7s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_saemix_parent.R:143'): 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 [1.4s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.7s]
+✔ | 10 | Fitting the SFORB model [3.9s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s]
-✔ | 9 | Hypothesis tests [8.1s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ | 9 | Hypothesis tests [8.2s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 260.9 s
+Duration: 280.1 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
• Fitting with saemix takes around 10 minutes when using deSolve (1)
• This still takes almost 2.5 minutes although we do not solve ODEs (1)
-[ FAIL 1 | WARN 0 | SKIP 3 | PASS 269 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ]

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