From 9e346fabe99de71b21ef085be102027cfa774910 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Aug 2022 12:58:35 +0200 Subject: Batch processing for hierarchical fits - 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs --- log/test.log | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 67ba8841..8be4a512 100644 --- a/log/test.log +++ b/log/test.log @@ -1,11 +1,11 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.3s] +✔ | 5 | Analytical solutions for coupled models [3.4s] ✔ | 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 [32.9s] +✔ | 1 12 | Dimethenamid data from 2018 [32.4s] ──────────────────────────────────────────────────────────────────────────────── 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 @@ -16,6 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ✔ | 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] +✔ | 5 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] ✔ | 1 12 | Nonlinear mixed-effects models [0.2s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits @@ -27,23 +28,23 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.4s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.8s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] -✔ | 16 | Plotting [10.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] +✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 28 | saemix parent models [182.2s] +✔ | 28 | saemix parent models [181.2s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] -✔ | 7 | Fitting the SFORB model [3.9s] +✔ | 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 [7.7s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 9 | Hypothesis tests [7.8s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 266.8 s +Duration: 279.6 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 0 | WARN 0 | SKIP 2 | PASS 228 ] +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 233 ] -- cgit v1.2.1