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authorJohannes Ranke <jranke@uni-bremen.de>2021-06-17 13:58:34 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-06-17 13:58:34 +0200
commit05baf3bf92cba127fd2319b779db78be86170e5e (patch)
tree98b0c8c63badd2421afa5ebaf12530290ac9c571 /test.log
parent28197d5fcbaf85b39f4c032b8180d68b6f6a01b3 (diff)
Let backtransform_odeparms handle nlmixr formation fractions
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
Diffstat (limited to 'test.log')
-rw-r--r--test.log45
1 files changed, 24 insertions, 21 deletions
diff --git a/test.log b/test.log
index f2a60729..6ef8191f 100644
--- a/test.log
+++ b/test.log
@@ -3,17 +3,17 @@ Loading required package: parallel
ℹ Testing mkin
✔ | OK F W S | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.3 s]
+✔ | 5 | Analytical solutions for coupled models [3.5 s]
✔ | 5 | Calculation of Akaike weights
✔ | 2 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [1.3 s]
+✔ | 12 | Confidence intervals and p-values [1.0 s]
✔ | 14 | Error model fitting [4.7 s]
✔ | 5 | Time step normalisation
-✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s]
+✔ | 4 | Calculation of FOCUS chi2 error levels [0.6 s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
-✔ | 35 1 | Nonlinear mixed-effects models [27.1 s]
+✔ | 35 1 | Nonlinear mixed-effects models [26.9 s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_mixed.R:161:3): saem results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
@@ -21,33 +21,36 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 2 | Test dataset classes mkinds and mkindsg
✔ | 10 | Special cases of mkinfit calls [0.4 s]
✔ | 1 | mkinfit features [0.3 s]
-✔ | 8 | mkinmod model generation and printing [0.3 s]
+✔ | 8 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.3 s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.1 s]
-✖ | 14 2 | Plotting [1.9 s]
+✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.3 s]
────────────────────────────────────────────────────────────────────────────────
-Failure (test_plot.R:40:5): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Figures don't match: mixed-model-fit-for-saem-object-with-saemix-transformations.svg
-
-
-Failure (test_plot.R:55:5): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Figures don't match: mixed-model-fit-for-saem-object-with-mkin-transformations.svg
+Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated
+Reason: getRversion() >= "4.1.0" is TRUE
+Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated
+Reason: getRversion() >= "4.1.0" is TRUE
+────────────────────────────────────────────────────────────────────────────────
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.1 s]
+✔ | 0 1 | Plotting [0.8 s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_plot.R:18:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Reason: getRversion() >= "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
-✔ | 7 | Fitting the SFORB model [3.9 s]
+✔ | 7 | Fitting the SFORB model [3.8 s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Summary [0.1 s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
-✔ | 9 | Hypothesis tests [8.2 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
+✔ | 9 | Hypothesis tests [8.5 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 70.0 s
+Duration: 68.2 s
── Skipped tests ──────────────────────────────────────────────────────────────
-● Fitting with saemix takes around 10 minutes when using deSolve (1)
+• Fitting with saemix takes around 10 minutes when using deSolve (1)
+• getRversion() >= "4.1.0" is TRUE (3)
-[ FAIL 2 | WARN 0 | SKIP 1 | PASS 204 ]
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 188 ]

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