Make saemix and corresponding tests optional

Address release critical check and test issues

1 files changed, 21 insertions, 21 deletions

diff --git a/tests/testthat/summary_nlme_biphasic_s.txt b/tests/testthat/summary_nlme_biphasic_s.txt
index f9171748..65aead62 100644
--- a/tests/testthat/summary_nlme_biphasic_s.txt
+++ b/tests/testthat/summary_nlme_biphasic_s.txt
@@ -17,15 +17,15 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in test time 0 s using 2 iterations
+Fitted in test time 0 s using 3 iterations
 
 Variance model: Constant variance 
 
 Mean of starting values for individual parameters:
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-         100.70           -6.30           -0.08           -3.09           -3.95 
+         100.70           -5.35           -0.08           -2.68           -4.37 
        g_qlogis 
-           0.03 
+          -0.33 
 
 Fixed degradation parameter values:
      value  type
@@ -34,40 +34,40 @@ m1_0     0 state
 Results:
 
    AIC  BIC logLik
-  2711 2766  -1343
+  2683 2738  -1329
 
 Optimised, transformed parameters with symmetric confidence intervals:
                 lower   est.  upper
-parent_0         99.5 100.37 101.23
-log_k_m1         -6.5  -6.23  -5.94
-f_parent_qlogis  -0.2  -0.08   0.08
-log_k1           -3.6  -3.22  -2.84
-log_k2           -4.5  -4.10  -3.68
-g_qlogis         -0.4  -0.10   0.17
+parent_0         99.6 100.43 101.26
+log_k_m1         -5.5  -5.34  -5.18
+f_parent_qlogis  -0.3  -0.08   0.09
+log_k1           -3.2  -2.90  -2.60
+log_k2           -4.6  -4.34  -4.07
+g_qlogis         -0.5  -0.19   0.08
 
 Correlation: 
                 prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-log_k_m1        -0.185                            
-f_parent_qlogis -0.161  0.405                     
-log_k1           0.056 -0.014 -0.016              
-log_k2           0.025  0.011 -0.004  0.026       
-g_qlogis        -0.032 -0.046 -0.012 -0.109 -0.103
+log_k_m1        -0.177                            
+f_parent_qlogis -0.164  0.385                     
+log_k1           0.108 -0.017 -0.025              
+log_k2           0.036  0.054  0.008  0.096       
+g_qlogis        -0.068 -0.110 -0.030 -0.269 -0.267
 
 Random effects:
  Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1)
  Level: ds
  Structure: Diagonal
         parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual
-StdDev:        1    2e-04             0.3    0.7    0.8      0.3        3
+StdDev:        1      0.1             0.3    0.6    0.5      0.3        3
 
 
 Backtransformed parameters with asymmetric confidence intervals:
                lower  est. upper
 parent_0       1e+02 1e+02 1e+02
-k_m1           1e-03 2e-03 3e-03
+k_m1           4e-03 5e-03 6e-03
 f_parent_to_m1 4e-01 5e-01 5e-01
-k1             3e-02 4e-02 6e-02
-k2             1e-02 2e-02 3e-02
+k1             4e-02 6e-02 7e-02
+k2             1e-02 1e-02 2e-02
 g              4e-01 5e-01 5e-01
 
 Resulting formation fractions:
@@ -77,5 +77,5 @@ parent_sink 0.5
 
 Estimated disappearance times:
        DT50 DT90 DT50back DT50_k1 DT50_k2
-parent   27  105       31      17      42
-m1      352 1171       NA      NA      NA
+parent   26  131       39      13      53
+m1      144  479       NA      NA      NA