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ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
✔ | 5 | Analytical solutions for coupled models [3.3s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
✔ | 1 12 | Dimethenamid data from 2018 [32.2s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_dmta.R:98:3): 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 [5.1s]
✔ | 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 [0.4s]
✔ | 1 | Fitting the logistic model [0.2s]
✖ | 1 6 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_mhmkin.R:41:3): Multiple hierarchical kinetic models can be fitted and diagnosed
Results have changed from known value recorded in 'summary_hfit_sfo_tc.txt'.
old | new
[45] "" | "" [45]
[46] "Variance model:" | "Variance model:" [46]
[47] " est. lower upper" | " est. lower upper" [47]
[48] "a.1 0.91 0.64 1.17" - "a.1 0.90 0.64 1.17" [48]
[49] "b.1 0.05 0.04 0.06" | "b.1 0.05 0.04 0.06" [49]
[50] "" | "" [50]
[51] "Backtransformed parameters:" | "Backtransformed parameters:" [51]
────────────────────────────────────────────────────────────────────────────────
✖ | 1 1 11 | Nonlinear mixed-effects models [0.3s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_mixed.R:8:3): Print methods work
Results have changed from known value recorded in 'print_sfo_saem_1.txt'.
old[7:19] vs new[7:19]
""
"Likelihood computed by importance sampling"
" AIC BIC logLik"
- " 1311 1315 -649"
+ " 1312 1316 -650"
""
"Fitted parameters:"
" estimate lower upper"
- "parent_0 1e+02 99.13 1e+02"
+ "parent_0 1e+02 99.28 1e+02"
"k_parent 4e-02 0.03 4e-02"
"a.1 9e-01 0.75 1e+00"
and 3 more ...
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 [0.4s]
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.4s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.9s]
✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s]
✔ | 16 | Plotting [10.2s]
✔ | 4 | Residuals extracted from mkinfit models
✔ | 28 | saemix parent models [181.5s]
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
✔ | 11 | Processing of residue series
✔ | 7 | Fitting the SFORB model [3.7s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
✔ | 9 | Hypothesis tests [8.3s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 280.7 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 2 | WARN 0 | SKIP 2 | PASS 244 ]
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