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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-14 20:03:42 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-14 20:03:42 +0100
commit21ad91256dc29423bd905de5c298fd23862b1f3b (patch)
tree225e2f69ed75b96e5528bcf7b8f25eb3864b75da /log/test.log
parent0db7df4bf632a013099b17d5e817a7dc7146c394 (diff)
Automatic starting parameters for saem.mmkin
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
Diffstat (limited to 'log/test.log')
-rw-r--r--log/test.log32
1 files changed, 16 insertions, 16 deletions
diff --git a/log/test.log b/log/test.log
index 874d6e24..f20a7f18 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,45 +1,45 @@
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 [3.2s]
✔ | 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 [31.5s]
+✔ | 1 12 | Dimethenamid data from 2018 [32.1s]
────────────────────────────────────────────────────────────────────────────────
-Skip (test_dmta.R:98:3): 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 [5.0s]
+✔ | 14 | Error model fitting [4.9s]
✔ | 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]
+✔ | 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 [24.0s]
✔ | 1 12 | Nonlinear mixed-effects models [0.3s]
────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:74:3): 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 [0.5s]
✔ | 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 [36.3s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s]
-✔ | 16 | Plotting [10.1s]
+✔ | 3 | Model predictions with mkinpredict [0.4s]
+✔ | 7 | Multistart method for saem.mmkin models [36.7s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ | 16 | Plotting [9.8s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 37 | saemix parent models [71.5s]
+✔ | 1 36 | saemix parent models [66.4s]
────────────────────────────────────────────────────────────────────────────────
-Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem
+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 [1.4s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.8s]
+✔ | 10 | 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) [2.2s]
@@ -47,11 +47,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 216.0 s
+Duration: 211.1 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 3 | PASS 268 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 267 ]

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