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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 [31.6s]
────────────────────────────────────────────────────────────────────────────────
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 [4.8s]
✔ | 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]
✔ | 1 | Fitting the logistic model [0.2s]
✖ | 1 7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_mhmkin.R:27:3): Multiple hierarchical kinetic models can be fitted and diagnosed
illparms(hfit_sfo_tc) not equal to character(0).
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
target is illparms.saem.mmkin, current is character
────────────────────────────────────────────────────────────────────────────────
✔ | 1 12 | Nonlinear mixed-effects models [0.3s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_mixed.R:74:3): 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 [0.3s]
✔ | 7 | Multistart method for saem.mmkin models [35.7s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s]
✔ | 16 | Plotting [10.1s]
✔ | 4 | Residuals extracted from mkinfit models
✖ | 3 1 34 | saemix parent models [70.9s]
────────────────────────────────────────────────────────────────────────────────
Failure (test_saemix_parent.R:12:3): Parent fits using saemix are correctly implemented
illparms(sfo_saem_1) not equal to "sd(parent_0)".
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
target is illparms.saem.mmkin, current is character
Failure (test_saemix_parent.R:14:3): Parent fits using saemix are correctly implemented
illparms(sfo_saem_1_reduced) not equal to character(0).
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
target is illparms.saem.mmkin, current is character
Failure (test_saemix_parent.R:25:3): Parent fits using saemix are correctly implemented
illparms(sfo_saem_1_mkin) not equal to "sd(parent_0)".
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
target is illparms.saem.mmkin, current is character
Skip (test_saemix_parent.R:153:3): 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 [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 [8.0s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 204.9 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 4 | WARN 0 | SKIP 3 | PASS 259 ]
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