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ℹ Loading mkin
Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
✔ | 5 | Analytical solutions for coupled models [14.4s]
✔ | 5 | Calculation of Akaike weights
✔ | 2 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
⠋ | 1 | Dimethenamid data from 2018
✔ | 1 27 | Dimethenamid data from 2018 [124.8s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_dmta.R:164:3): 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 [6.8s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s]
✔ | 1 | Fitting the logistic model [0.3s]
⠇ | 1 8 | Nonlinear mixed-effects models
✖ | 1 1 13 | Nonlinear mixed-effects models [1.5s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_mixed.R:5:3): Print methods work
Results have changed from known value recorded in 'print_mmkin_dfop_1_mixed.txt'.
old[18:21] vs new[18:21]
""
"Mean fitted parameters:"
"parent_0 log_k1 log_k2 g_qlogis "
- " 100.06 -2.68 -5.57 0.01 "
+ " 100.06 -2.68 -5.58 0.01 "
Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
✔ | 3 | Test dataset classes mkinds and mkindsg
✔ | 10 | Special cases of mkinfit calls [0.6s]
✔ | 3 | mkinfit features [1.1s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.3s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s]
✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s]
✖ | 2 14 | Plotting [1.5s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_plot.R:42:3): 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:42:2
3. testthat::expect_snapshot_file(...)
Failure (test_plot.R:50:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
Snapshot of `testcase` to 'plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
Run `testthat::snapshot_review('plot/')` to review changes
Backtrace:
1. vdiffr::expect_doppelganger(...)
at test_plot.R:50:2
3. testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
✔ | 23 | saemix_parent [28.7s]
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.2s]
✔ | 7 | Fitting the SFORB model [16.1s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Summary [0.1s]
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [19.0s]
✔ | 9 | Hypothesis tests [67.6s]
✔ | 2 | tffm0
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 314.2 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)
[ FAIL 3 | WARN 0 | SKIP 2 | PASS 237 ]
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