path: root/log/test.log

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
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✔ |        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 ]