Fix tests and rerun

1 files changed, 65 insertions, 60 deletions

diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index da3276e1..2b0210c0 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -1,77 +1,82 @@
-saemix version used for fitting:      3.1.9000 
-mkin version used for pre-fitting:  0.9.50.4 
-R version used for fitting:         4.0.3 
-Date of fit:     Wed Dec  9 08:16:28 2020 
-Date of summary: Wed Dec  9 08:23:19 2020 
+mkin version used for fitting:    Dummy 0.0 for testing 
+R version used for fitting:       Dummy R version for testing 
+Date of fit:     Dummy date for testing 
+Date of summary: Dummy date for testing 
 
 Equations:
 d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
            * parent
-d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
-           * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
-           exp(-k2 * time))) * parent - k_m1 * m1
-
-Data:
-509 observations of 2 variable(s) grouped in 15 datasets
 
 Model predictions using solution type analytical 
 
-Fitted in 10.222 s using 300, 100 iterations
+Fitted using test 0 model solutions performed in test time 0 s
+
+Error model: Constant variance 
 
-Variance model: Constant variance 
+Error model algorithm: OLS 
 
-Mean of starting values for individual parameters:
-      parent_0           k_m1 f_parent_to_m1             k1             k2 
-  1.007005e+02   1.837381e-03   4.803953e-01   4.534096e-02   1.918378e-02 
-             g 
-  5.068235e-01 
+Starting values for parameters to be optimised:
+         value   type
+parent_0 85.10  state
+k1        0.10 deparm
+k2        0.01 deparm
+g         0.50 deparm
 
-Fixed degradation parameter values:
+Starting values for the transformed parameters actually optimised:
+             value lower upper
+parent_0 85.100000  -Inf   Inf
+log_k1   -2.302585  -Inf   Inf
+log_k2   -4.605170  -Inf   Inf
+g_qlogis  0.000000  -Inf   Inf
+
+Fixed parameter values:
 None
 
 Results:
 
-Likelihood computed by importance sampling
-   AIC  BIC logLik
-  2692 2702  -1333
-
-Optimised parameters:
-                    est.     lower     upper
-parent_0       1.002e+02 99.302986 1.011e+02
-k_m1           2.182e-03  0.001576 2.788e-03
-f_parent_to_m1 4.883e-01  0.447687 5.289e-01
-k1             4.014e-02  0.023941 5.634e-02
-k2             1.517e-02  0.008507 2.184e-02
-g              5.007e-01  0.380534 6.208e-01
-
-Correlation: 
-               prnt_0 k_m1   f_p__1 k1     k2    
-k_m1           -0.152                            
-f_parent_to_m1 -0.138  0.396                     
-k1              0.085 -0.036 -0.026              
-k2              0.005  0.067  0.018 -0.043       
-g              -0.075 -0.113 -0.029 -0.248 -0.263
-
-Random effects:
-                    est.   lower  upper
-SD.parent_0       1.2293  0.3904 2.0682
-SD.k_m1           0.1383 -0.4780 0.7545
-SD.f_parent_to_m1 0.2843  0.1746 0.3940
-SD.k1             0.7097  0.4220 0.9974
-SD.k2             0.7829  0.4712 1.0946
-SD.g              0.2666 -0.3260 0.8592
-
-Variance model:
-     est. lower upper
-a.1 2.749 2.569 2.929
-
-Resulting formation fractions:
-                ff
-parent_m1   0.4883
-parent_sink 0.5117
+       AIC      BIC    logLik
+  29.02372 30.00984 -9.511861
+
+Optimised, transformed parameters with symmetric confidence intervals:
+         Estimate Std. Error   Lower   Upper
+parent_0  85.0000    0.66620 83.1500 86.8500
+log_k1    -0.7775    0.03380 -0.8713 -0.6836
+log_k2    -4.0260    0.13100 -4.3890 -3.6620
+g_qlogis   1.7660    0.08218  1.5380  1.9940
+sigma      0.6962    0.16410  0.2406  1.1520
+
+Parameter correlation:
+[1] "Correlation matrix is platform dependent, not tested"
+
+Backtransformed parameters:
+Confidence intervals for internally transformed parameters are asymmetric.
+t-test (unrealistically) based on the assumption of normal distribution
+for estimators of untransformed parameters.
+         Estimate t value    Pr(>t)    Lower    Upper
+parent_0 85.00000 127.600 1.131e-08 83.15000 86.85000
+k1        0.45960  29.580 3.887e-06  0.41840  0.50480
+k2        0.01785   7.636 7.901e-04  0.01241  0.02568
+g         0.85390  83.310 6.221e-08  0.82310  0.88020
+sigma     0.69620   4.243 6.618e-03  0.24060  1.15200
+
+FOCUS Chi2 error levels in percent:
+         err.min n.optim df
+All data   2.661       4  5
+parent     2.661       4  5
 
 Estimated disappearance times:
-         DT50   DT90 DT50back DT50_k1 DT50_k2
-parent  27.07  110.1    33.14   17.27   45.68
-m1     317.69 1055.4       NA      NA      NA
+        DT50  DT90 DT50back DT50_k1 DT50_k2
+parent 1.887 21.25    6.397   1.508   38.83
+
+Data:
+ time variable observed predicted residual
+    0   parent     85.1    85.003  0.09726
+    1   parent     57.9    58.039 -0.13912
+    3   parent     29.9    30.054 -0.15351
+    7   parent     14.6    13.866  0.73388
+   14   parent      9.7     9.787 -0.08657
+   28   parent      6.6     7.532 -0.93205
+   63   parent      4.0     4.033 -0.03269
+   91   parent      3.9     2.447  1.45348
+  119   parent      0.6     1.484 -0.88424