diff options
| -rw-r--r-- | R/logLik.mkinfit.R | 1 | ||||
| -rw-r--r-- | log/test_dev.log | 61 |
2 files changed, 33 insertions, 29 deletions
diff --git a/R/logLik.mkinfit.R b/R/logLik.mkinfit.R index 7cc10234..abf8517c 100644 --- a/R/logLik.mkinfit.R +++ b/R/logLik.mkinfit.R @@ -37,6 +37,7 @@ logLik.mkinfit <- function(object, ...) { val <- object$logLik # Number of estimated parameters attr(val, "df") <- length(object$bparms.optim) + length(object$errparms) + attr(val, "nobs") <- nobs(object) class(val) <- "logLik" return(val) } diff --git a/log/test_dev.log b/log/test_dev.log index 24905a1a..527d28ed 100644 --- a/log/test_dev.log +++ b/log/test_dev.log @@ -1,54 +1,57 @@ -ℹ Loading mkin -Loading required package: parallel ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [14.6s] +✔ | 5 | Analytical solutions for coupled models [3.2s] ✔ | 5 | Calculation of Akaike weights -✔ | 2 | Export dataset for reading into CAKE +✔ | 3 | 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 [116.1s] +✔ | 1 12 | Dimethenamid data from 2018 [31.3s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +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 [6.6s] +✔ | 14 | Error model fitting [5.2s] ✔ | 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] -⠋ | 11 | Nonlinear mixed-effects models -✔ | 1 14 | Nonlinear mixed-effects models [1.3s] +✔ | 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] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.5s] +✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +Skip ('test_mixed.R:74'): 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] +✔ | 10 | Special cases of mkinfit calls [0.5s] +✔ | 3 | mkinfit features [0.7s] ✔ | 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 [8.7s] -✔ | 16 | Plotting [1.4s] +✔ | 9 | Multistart method for saem.mmkin models [35.2s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] +✔ | 16 | Plotting [10.0s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 23 | saemix parent models [28.4s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s] -✔ | 7 | Fitting the SFORB model [16.9s] +✔ | 1 36 | saemix parent models [63.3s] +──────────────────────────────────────────────────────────────────────────────── +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 [1.3s] +✔ | 11 | Processing of residue series +✔ | 10 | Fitting the SFORB model [3.5s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s] -✔ | 9 | Hypothesis tests [78.9s] -✔ | 2 | tffm0 +✔ | 5 | Summary [0.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] +✔ | 9 | Hypothesis tests [7.5s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 315.9 s +Duration: 204.4 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 0 | WARN 0 | SKIP 2 | PASS 240 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ] |