From 478c6d5eec4c84b22b43adcbdf36888b302ead00 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 6 Dec 2022 10:33:24 +0100
Subject: Some parplot improvements
llquant argument, improved legend text, tests
---
log/test.log | 41 +++++++++++++++++++++++++----------------
1 file changed, 25 insertions(+), 16 deletions(-)
(limited to 'log')
diff --git a/log/test.log b/log/test.log
index 5764f209..7614b136 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,22 +1,22 @@
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 [1.1s]
-✔ | 1 12 | Dimethenamid data from 2018 [31.9s]
+✔ | 1 12 | Dimethenamid data from 2018 [32.0s]
────────────────────────────────────────────────────────────────────────────────
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 [4.9s]
+✔ | 14 | Error model fitting [4.8s]
✔ | 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 [0.3s]
✔ | 1 | Fitting the logistic model [0.2s]
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [41.4s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s]
✔ | 1 11 | Nonlinear mixed-effects models [13.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
@@ -26,32 +26,41 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 10 | Special cases of mkinfit calls [0.6s]
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
-✔ | 3 | Model predictions with mkinpredict [0.3s]
-✔ | 12 | Multistart method for saem.mmkin models [47.5s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s]
-✔ | 15 | Plotting [10.2s]
+✔ | 3 | Model predictions with mkinpredict [0.4s]
+✖ | 1 11 | Multistart method for saem.mmkin models [46.7s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_multistart.R:56'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo)
+ at test_multistart.R:56:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s]
+✔ | 15 | Plotting [10.1s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [73.0s]
+✔ | 1 36 | saemix parent models [73.6s]
────────────────────────────────────────────────────────────────────────────────
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 [1.5s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.9s]
+✔ | 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]
-✔ | 9 | Hypothesis tests [8.4s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s]
+✔ | 9 | Hypothesis tests [8.1s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 261.1 s
+Duration: 260.9 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 270 ]
+[ FAIL 1 | WARN 0 | SKIP 3 | PASS 269 ]
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