mixed.mmkin and test coverage

1 files changed, 23 insertions, 17 deletions

diff --git a/test.log b/test.log
index c977d6a0..70011abb 100644
--- a/test.log
+++ b/test.log
@@ -2,48 +2,54 @@ Loading mkin
 Loading required package: parallel
 Testing mkin
 ✔ |  OK F W S | Context
-✔ |   4       | AIC calculation
+✔ |   5       | AIC calculation
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
-✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s]
+✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
+✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
 ✔ |   7       | Fitting the SFORB model [3.5 s]
-✔ |   5       | Analytical solutions for coupled models [3.1 s]
+✔ |   5       | Analytical solutions for coupled models [3.2 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [1.0 s]
-✔ |  14       | Error model fitting [4.7 s]
+✔ |  14       | Confidence intervals and p-values [1.2 s]
+✔ |  14       | Error model fitting [4.5 s]
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
 ✔ |   1       | mkinfit features [0.3 s]
 ✔ |  12       | Special cases of mkinfit calls [0.7 s]
-✔ |   8       | mkinmod model generation and printing [0.3 s]
+✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
-✔ |  14     2 | Evaluations according to 2015 NAFTA guidance [1.2 s]
+✔ |  14     2 | Evaluations according to 2015 NAFTA guidance [1.3 s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_nafta.R:26:5): Test data from Appendix B are correctly evaluated
+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:55:5): Test data from Appendix D are correctly evaluated
+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 [8.0 s]
+✔ |   9       | Nonlinear mixed-effects models [7.9 s]
 ✔ |   0     1 | Plotting [0.7 s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_plot.R:25:3): Plotting mkinfit and mmkin objects is reproducible
+Skip (test_plot.R:28:3): Plotting mkinfit and mmkin 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 [1.7 s]
-✔ |   4       | Summary [0.2 s]
+✔ |  13     1 | Nonlinear mixed effects models fitted with SAEM from saemix [19.0 s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_saem.R:103:1): Simple models with metabolite can be fitted with saemix
+Reason: empty test
+────────────────────────────────────────────────────────────────────────────────
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ |   9       | Hypothesis tests [7.2 s]
+✔ |   9       | Hypothesis tests [7.3 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 39.8 s
+Duration: 59.7 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
+● empty test (1)
 ● getRversion() < "4.1.0"  is TRUE (3)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 146 ]
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 164 ]