From 17af45b984d348505527140470c7fff204748ea6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 12 Sep 2025 22:16:13 +0200 Subject: Facilitate centering covariates The motivation for this is to obtain confidence intervals for covariate dependent parameters that are valid for a median/mean value of the covariate. Implementation by adding an argument to the 'saem' function, and adapting the relevant functions working with 'saem' objects. Vignettes, the template and tests were updated to use the new functionality. --- log/test.log | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 7bf36295..1b7f5c00 100644 --- a/log/test.log +++ b/log/test.log @@ -4,29 +4,29 @@ ✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.4s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.6s] ✔ | 12 | Confidence intervals and p-values ✔ | 1 | Solutions with deSolve -✔ | 1 12 | Dimethenamid data from 2018 [13.1s] -✔ | 14 | Error model fitting [2.6s] +✔ | 1 12 | Dimethenamid data from 2018 [14.1s] +✔ | 14 | Error model fitting [2.8s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.9s] -✔ | 2 16 | Nonlinear mixed-effects models [145.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [20.5s] +✔ | 2 20 | Nonlinear mixed-effects models [144.7s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 4 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.4s] +✔ | 12 | Multistart method for saem.mmkin models [23.7s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [4.0s] -✔ | 15 | Plotting [4.7s] +✔ | 9 | Nonlinear mixed-effects models with nlme [4.3s] +✔ | 15 | Plotting [4.8s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [36.0s] +✔ | 1 38 | saemix parent models [35.6s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [1.7s] @@ -38,15 +38,15 @@ ✔ | 2 | water-sediment ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 265.4 s +Duration: 267.4 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1): 'test_dmta.R:88:3' • Fitting with saemix takes around 10 minutes when using deSolve (1): 'test_mixed.R:80:3' -• This is seldom used, so save some time (1): 'test_mixed.R:135:3' +• This is seldom used, so save some time (1): 'test_mixed.R:155:3' • This still takes almost 2.5 minutes although we do not solve ODEs (1): 'test_saemix_parent.R:143:3' -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 287 ] +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 291 ] -- cgit v1.2.1