Rerun test with saemix 3.1 from CRAN

Apparently, the change I introduced into saemix
saemixdevelopment/saemixextension#34
to fix error model parameters to positive values slightly influences the
results. So this is now with the CRAN version to keep test results
in sync with Travis

3 files changed, 14 insertions, 14 deletions

diff --git a/log/test.log b/log/test.log
index cb123776..efa30d17 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 [3.4s]
 ✔ |         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 [32.5s]
+✔ |        12 | Confidence intervals and p-values [1.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.9s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): 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 [5.1s]
+✔ |        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]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.6s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
@@ -28,20 +28,20 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.8s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
 ✔ |        16 | Plotting [10.0s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        28 | saemix parent models [183.3s]
+✔ |        28 | saemix parent models [180.2s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ |         7 | Fitting the SFORB model [3.7s]
+✔ |         7 | Fitting the SFORB model [3.6s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [8.1s]
+✔ |         9 | Hypothesis tests [7.8s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 282.2 s
+Duration: 277.4 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/tests/testthat/print_sfo_saem_1.txt b/tests/testthat/print_sfo_saem_1.txt
index 34eea058..a11e1e96 100644
--- a/tests/testthat/print_sfo_saem_1.txt
+++ b/tests/testthat/print_sfo_saem_1.txt
@@ -7,13 +7,13 @@ Data:
 
 Likelihood computed by importance sampling
    AIC  BIC logLik
-  1312 1316   -650
+  1311 1315   -649
 
 Fitted parameters:
             estimate lower upper
-parent_0       1e+02 99.28 1e+02
+parent_0       1e+02 99.13 1e+02
 k_parent       4e-02  0.03 4e-02
 a.1            9e-01  0.75 1e+00
 b.1            5e-02  0.04 5e-02
-SD.parent_0    2e-01 -6.33 7e+00
+SD.parent_0    7e-01 -1.09 3e+00
 SD.k_parent    3e-01  0.20 4e-01
diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt
index e3e2f7e4..ad701cee 100644
--- a/tests/testthat/summary_hfit_sfo_tc.txt
+++ b/tests/testthat/summary_hfit_sfo_tc.txt
@@ -45,7 +45,7 @@ SD.log_k_parent  0.3   0.1   0.4
 
 Variance model:
     est. lower upper
-a.1 0.90  0.64  1.17
+a.1 0.91  0.64  1.17
 b.1 0.05  0.04  0.06
 
 Backtransformed parameters: