Log-Cholesky parameterisation as default in nlme.mmkin

1 files changed, 13 insertions, 9 deletions

diff --git a/test.log b/test.log
index 67fd66c4..84a8748e 100644
--- a/test.log
+++ b/test.log
@@ -6,11 +6,11 @@ Testing mkin
 ✔ |   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]
-✔ |   7       | Fitting the SFORB model [3.2 s]
-✔ |   5       | Analytical solutions for coupled models [2.9 s]
+✔ |   7       | Fitting the SFORB model [3.4 s]
+✔ |   5       | Analytical solutions for coupled models [3.1 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  10       | Confidence intervals and p-values [1.0 s]
-✔ |  14       | Error model fitting [4.3 s]
+✔ |  14       | Error model fitting [4.4 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
@@ -26,24 +26,28 @@ Reason: getRversion() < "4.1.0"  is TRUE
 Skip (test_nafta.R:55:5): Test data from Appendix D are correctly evaluated
 Reason: getRversion() < "4.1.0"  is TRUE
 ────────────────────────────────────────────────────────────────────────────────
-✔ |   9       | Nonlinear mixed-effects models [7.8 s]
+✖ |   7 1     | Nonlinear mixed-effects models [8.0 s]
+────────────────────────────────────────────────────────────────────────────────
+FAILURE (test_nlme.R:90:3): nlme_function works correctly
+`tmp <- update(m_nlme_mmkin)` did not produce any warnings.
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   0     1 | Plotting [0.7 s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_plot.R:25:3): 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 [1.4 s]
+✔ |   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) [2.0 s]
-✔ |   9       | Hypothesis tests [6.4 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
+✔ |   9       | Hypothesis tests [7.2 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 36.9 s
+Duration: 38.9 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 ● getRversion() < "4.1.0"  is TRUE (3)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 146 ]
+[ FAIL 1 | WARN 0 | SKIP 3 | PASS 144 ]