Adapt tests, vignettes and examples

- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit

1 files changed, 292 insertions, 152 deletions

diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index 7abde0b6..5327b3f6 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -1,148 +1,148 @@
-parent_0 log_k1 log_k2 g_ilr 
+parent_0 log_k1 log_k2 g_ilr sigma 
 85.1 -2.302585 -4.60517 0 
-Model cost at call  1 :  7391.39 
+Negative log-likelihood at call 1: 7391.39
 85.1 -2.302585 -4.60517 0 
 85.1 -2.302585 -4.60517 0 
-Model cost at call  3 :  7391.389 
+Negative log-likelihood at call 3: 7391.389
 85.1 -2.302585 -4.60517 0 
-Model cost at call  4 :  7391.389 
+Negative log-likelihood at call 4: 7391.389
 85.1 -2.302585 -4.60517 1.490116e-08 
 85.06371 -1.77328 -4.250366 0.7698268 
-Model cost at call  6 :  2000.127 
+Negative log-likelihood at call 6: 2000.127
 85.06375 -1.77328 -4.250366 0.7698268 
 85.06371 -1.773322 -4.250366 0.7698268 
 85.06371 -1.77328 -4.250408 0.7698268 
 85.06371 -1.77328 -4.250366 0.7697847 
 85.03542 -0.9608523 -4.11546 1.336361 
-Model cost at call  11 :  32.97798 
+Negative log-likelihood at call 11: 32.97798
 85.03542 -0.9608523 -4.11546 1.336361 
 85.03542 -0.9608526 -4.11546 1.336361 
 85.03542 -0.9608523 -4.11546 1.336361 
 85.03542 -0.9608523 -4.11546 1.336361 
 85.03704 -0.256064 -4.273512 0.6447755 
 85.03285 -0.7822828 -4.127513 1.312494 
-Model cost at call  17 :  5.348133 
+Negative log-likelihood at call 17: 5.348133
 85.03286 -0.7822828 -4.127513 1.312494 
-Model cost at call  18 :  5.348132 
+Negative log-likelihood at call 18: 5.348132
 85.03285 -0.7822828 -4.127513 1.312494 
-Model cost at call  19 :  5.348131 
+Negative log-likelihood at call 19: 5.348131
 85.03285 -0.7822828 -4.127513 1.312494 
 85.03285 -0.7822828 -4.127513 1.312494 
-Model cost at call  21 :  5.348131 
+Negative log-likelihood at call 21: 5.348131
 85.02325 -0.74968 -4.059 1.14891 
 85.03127 -0.7909068 -4.114802 1.268157 
-Model cost at call  23 :  4.704445 
+Negative log-likelihood at call 23: 4.704445
 85.03127 -0.7909068 -4.114802 1.268157 
-Model cost at call  24 :  4.704444 
+Negative log-likelihood at call 24: 4.704444
 85.03127 -0.7909068 -4.114802 1.268157 
 85.03127 -0.7909068 -4.1148 1.268157 
-Model cost at call  26 :  4.704433 
+Negative log-likelihood at call 26: 4.704433
 85.03127 -0.7909068 -4.114802 1.268158 
 85.03001 -0.7801506 -4.069435 1.262797 
-Model cost at call  28 :  4.421625 
+Negative log-likelihood at call 28: 4.421625
 85.03001 -0.7801506 -4.069435 1.262797 
 85.03001 -0.7801507 -4.069435 1.262797 
-Model cost at call  30 :  4.421624 
+Negative log-likelihood at call 30: 4.421624
 85.03001 -0.7801506 -4.069435 1.262797 
 85.03001 -0.7801506 -4.069435 1.262797 
 85.02878 -0.7900844 -4.023945 1.256918 
 85.02964 -0.7857352 -4.054587 1.260236 
-Model cost at call  34 :  4.414346 
+Negative log-likelihood at call 34: 4.414346
 85.02964 -0.7857352 -4.054587 1.260236 
 85.02964 -0.7857351 -4.054587 1.260236 
-Model cost at call  36 :  4.414346 
+Negative log-likelihood at call 36: 4.414346
 85.02964 -0.7857352 -4.054588 1.260236 
 85.02964 -0.7857352 -4.054587 1.260236 
 85.02812 -0.7778128 -4.042219 1.25389 
-Model cost at call  39 :  4.372463 
+Negative log-likelihood at call 39: 4.372463
 85.02812 -0.7778128 -4.042219 1.25389 
 85.02812 -0.7778129 -4.042219 1.25389 
-Model cost at call  41 :  4.372462 
+Negative log-likelihood at call 41: 4.372462
 85.02812 -0.7778128 -4.042219 1.25389 
 85.02812 -0.7778128 -4.042219 1.25389 
 85.02419 -0.7765144 -4.02942 1.245094 
 85.0263 -0.7778419 -4.036021 1.249634 
-Model cost at call  45 :  4.369313 
+Negative log-likelihood at call 45: 4.369313
 85.0263 -0.7778419 -4.036021 1.249634 
 85.0263 -0.7778418 -4.036021 1.249634 
-Model cost at call  47 :  4.369313 
+Negative log-likelihood at call 47: 4.369313
 85.0263 -0.7778419 -4.036022 1.249634 
 85.0263 -0.7778419 -4.036021 1.249634 
-Model cost at call  49 :  4.369313 
+Negative log-likelihood at call 49: 4.369313
 85.02267 -0.7786811 -4.02967 1.252015 
-Model cost at call  50 :  4.365062 
+Negative log-likelihood at call 50: 4.365062
 85.02268 -0.7786811 -4.02967 1.252015 
 85.02267 -0.7786812 -4.02967 1.252015 
 85.02267 -0.7786811 -4.02967 1.252015 
-Model cost at call  53 :  4.365062 
+Negative log-likelihood at call 53: 4.365062
 85.02267 -0.7786811 -4.02967 1.252015 
 85.01633 -0.7763163 -4.027611 1.248897 
-Model cost at call  55 :  4.364078 
+Negative log-likelihood at call 55: 4.364078
 85.01633 -0.7763163 -4.027611 1.248897 
-Model cost at call  56 :  4.364078 
+Negative log-likelihood at call 56: 4.364078
 85.01633 -0.7763164 -4.027611 1.248897 
-Model cost at call  57 :  4.364077 
+Negative log-likelihood at call 57: 4.364077
 85.01633 -0.7763163 -4.027611 1.248897 
 85.01633 -0.7763163 -4.027611 1.248897 
 85.00894 -0.7777917 -4.026307 1.24772 
-Model cost at call  60 :  4.364052 
+Negative log-likelihood at call 60: 4.364052
 85.00894 -0.7777917 -4.026307 1.24772 
-Model cost at call  61 :  4.364052 
+Negative log-likelihood at call 61: 4.364052
 85.00894 -0.7777917 -4.026307 1.24772 
-Model cost at call  62 :  4.364052 
+Negative log-likelihood at call 62: 4.364052
 85.00894 -0.7777917 -4.026307 1.24772 
 85.00894 -0.7777917 -4.026307 1.24772 
-Model cost at call  64 :  4.364052 
+Negative log-likelihood at call 64: 4.364052
 85.00518 -0.7773082 -4.026004 1.248453 
-Model cost at call  65 :  4.362751 
+Negative log-likelihood at call 65: 4.362751
 85.00519 -0.7773082 -4.026004 1.248453 
 85.00518 -0.7773083 -4.026004 1.248453 
-Model cost at call  67 :  4.362751 
+Negative log-likelihood at call 67: 4.362751
 85.00518 -0.7773082 -4.026005 1.248453 
 85.00518 -0.7773082 -4.026004 1.248453 
 85.00134 -0.7776046 -4.025878 1.248775 
-Model cost at call  70 :  4.362721 
+Negative log-likelihood at call 70: 4.362721
 85.00135 -0.7776046 -4.025878 1.248775 
-Model cost at call  71 :  4.362721 
+Negative log-likelihood at call 71: 4.362721
 85.00134 -0.7776046 -4.025878 1.248775 
-Model cost at call  72 :  4.362721 
+Negative log-likelihood at call 72: 4.362721
 85.00134 -0.7776046 -4.025878 1.248775 
 85.00134 -0.7776046 -4.025878 1.248775 
 85.0032 -0.7774734 -4.0257 1.248643 
-Model cost at call  75 :  4.362715 
+Negative log-likelihood at call 75: 4.362715
 85.0032 -0.7774734 -4.0257 1.248643 
 85.0032 -0.7774734 -4.0257 1.248643 
-Model cost at call  77 :  4.362715 
+Negative log-likelihood at call 77: 4.362715
 85.0032 -0.7774735 -4.0257 1.248643 
 85.0032 -0.7774734 -4.0257 1.248643 
 85.0032 -0.7774734 -4.0257 1.248643 
 85.0032 -0.7774734 -4.0257 1.248643 
 85.00249 -0.7774909 -4.025911 1.248679 
-Model cost at call  82 :  4.362715 
+Negative log-likelihood at call 82: 4.362715
 85.0025 -0.7774909 -4.025911 1.248679 
-Model cost at call  83 :  4.362715 
+Negative log-likelihood at call 83: 4.362715
 85.00249 -0.7774909 -4.025911 1.248679 
 85.00249 -0.7774905 -4.025911 1.248679 
 85.00249 -0.7774914 -4.025911 1.248679 
-Model cost at call  86 :  4.362715 
+Negative log-likelihood at call 86: 4.362715
 85.00249 -0.7774909 -4.025911 1.248679 
 85.00249 -0.7774909 -4.025911 1.248679 
 85.00249 -0.7774909 -4.025911 1.248679 
 85.00249 -0.7774909 -4.025911 1.248679 
 85.00274 -0.7774922 -4.025821 1.248672 
-Model cost at call  91 :  4.362714 
+Negative log-likelihood at call 91: 4.362714
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00274 -0.7774922 -4.025821 1.248672 
-Model cost at call  93 :  4.362714 
+Negative log-likelihood at call 93: 4.362714
 85.00274 -0.7774921 -4.025821 1.248672 
-Model cost at call  94 :  4.362714 
+Negative log-likelihood at call 94: 4.362714
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00274 -0.7774922 -4.025821 1.248672 
 85.00273 -0.7774912 -4.025817 1.24867 
-Model cost at call  100 :  4.362714 
+Negative log-likelihood at call 100: 4.362714
 85.00275 -0.7774912 -4.025817 1.24867 
 85.00271 -0.7774912 -4.025817 1.24867 
 85.00273 -0.7774905 -4.025817 1.24867 
@@ -152,7 +152,7 @@ Model cost at call  100 :  4.362714
 85.00273 -0.7774912 -4.025817 1.248671 
 85.00273 -0.7774912 -4.025817 1.248669 
 85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  109 :  4.362714 
+Negative log-likelihood at call 109: 4.362714
 85.00276 -0.7774913 -4.025819 1.248671 
 85.00272 -0.7774913 -4.025819 1.248671 
 85.00274 -0.7774904 -4.025819 1.248671 
@@ -162,109 +162,249 @@ Model cost at call  109 :  4.362714
 85.00274 -0.7774913 -4.025819 1.248672 
 85.00274 -0.7774913 -4.025819 1.248669 
 85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  123 :  4.362714 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-IRLS based on variance estimates according to the two component error model
-Initial variance components are:
-sigma_low  rsd_high 
-  1.08984   0.00000 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  129 :  3.673061 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  132 :  3.673061 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00273 -0.7775309 -4.025818 1.24866 
-85.00274 -0.7774953 -4.025819 1.24867 
-85.00274 -0.7774917 -4.025819 1.248671 
-85.00274 -0.7774914 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  138 :  3.673061 
-85.00277 -0.7774913 -4.025819 1.248671 
-85.0027 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774744 -4.025819 1.248671 
-85.00274 -0.7775083 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025779 1.248671 
-85.00274 -0.7774913 -4.025858 1.248671 
-85.00274 -0.7774913 -4.025819 1.248702 
-85.00274 -0.7774913 -4.025819 1.248639 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  147 :  3.673061 
-85.00276 -0.7774913 -4.025819 1.248671 
-85.00271 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774906 -4.025819 1.248671 
-85.00274 -0.7774921 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025812 1.248671 
-85.00274 -0.7774913 -4.025825 1.248671 
-85.00274 -0.7774913 -4.025819 1.248672 
-85.00274 -0.7774913 -4.025819 1.248669 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Model cost at call  159 :  3.673061 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Iteration 1 yields variance estimates:
-sigma_low  rsd_high 
-0.7434091 0.0000000 
-Sum of squared differences to last variance (component) estimates: 0.12 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00273 -0.7775366 -4.025821 1.248652 
-85.00274 -0.7774959 -4.025819 1.248669 
-85.00274 -0.7774918 -4.025819 1.24867 
-85.00274 -0.7774914 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00279 -0.7774913 -4.025819 1.248671 
-85.00268 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774621 -4.025819 1.248671 
-85.00274 -0.7775206 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025761 1.248671 
-85.00274 -0.7774913 -4.025876 1.248671 
-85.00274 -0.7774913 -4.025819 1.248714 
-85.00274 -0.7774913 -4.025819 1.248627 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00273 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774908 -4.025819 1.248671 
-85.00274 -0.7774919 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025816 1.248671 
-85.00274 -0.7774913 -4.025822 1.248671 
-85.00274 -0.7774913 -4.025819 1.248672 
-85.00274 -0.7774913 -4.025819 1.24867 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-85.00274 -0.7774913 -4.025819 1.248671 
-Iteration 2 yields variance estimates:
-sigma_low  rsd_high 
-0.7434091 0.0000000 
-Sum of squared differences to last variance (component) estimates: 2.9e-16 
-Optimisation by method Port successfully terminated.
+85.00274 -0.7774913 -4.025819 1.248671 0.696237 
+85.00274 -0.7774913 -4.025819 1.248671 0.696237 
+85.00274 -0.7774913 -4.025819 1.248671 0.696237 
+93.50301 -0.7774913 -4.025819 1.248671 0.696237 
+76.50246 -0.7774913 -4.025819 1.248671 0.696237 
+89.25287 -0.7774913 -4.025819 1.248671 0.696237 
+80.7526 -0.7774913 -4.025819 1.248671 0.696237 
+87.12781 -0.7774913 -4.025819 1.248671 0.696237 
+82.87767 -0.7774913 -4.025819 1.248671 0.696237 
+86.06527 -0.7774913 -4.025819 1.248671 0.696237 
+83.9402 -0.7774913 -4.025819 1.248671 0.696237 
+85.00274 -0.6997422 -4.025819 1.248671 0.696237 
+85.00274 -0.8552405 -4.025819 1.248671 0.696237 
+85.00274 -0.7386168 -4.025819 1.248671 0.696237 
+85.00274 -0.8163659 -4.025819 1.248671 0.696237 
+85.00274 -0.758054 -4.025819 1.248671 0.696237 
+85.00274 -0.7969286 -4.025819 1.248671 0.696237 
+85.00274 -0.7677727 -4.025819 1.248671 0.696237 
+85.00274 -0.78721 -4.025819 1.248671 0.696237 
+85.00274 -0.7774913 -3.623237 1.248671 0.696237 
+85.00274 -0.7774913 -4.428401 1.248671 0.696237 
+85.00274 -0.7774913 -3.824528 1.248671 0.696237 
+85.00274 -0.7774913 -4.22711 1.248671 0.696237 
+85.00274 -0.7774913 -3.925173 1.248671 0.696237 
+85.00274 -0.7774913 -4.126464 1.248671 0.696237 
+85.00274 -0.7774913 -3.975496 1.248671 0.696237 
+85.00274 -0.7774913 -4.076142 1.248671 0.696237 
+85.00274 -0.7774913 -4.025819 1.373538 0.696237 
+85.00274 -0.7774913 -4.025819 1.123804 0.696237 
+85.00274 -0.7774913 -4.025819 1.311104 0.696237 
+85.00274 -0.7774913 -4.025819 1.186237 0.696237 
+85.00274 -0.7774913 -4.025819 1.279887 0.696237 
+85.00274 -0.7774913 -4.025819 1.217454 0.696237 
+85.00274 -0.7774913 -4.025819 1.264279 0.696237 
+85.00274 -0.7774913 -4.025819 1.233062 0.696237 
+85.00274 -0.7774913 -4.025819 1.248671 0.7658608 
+85.00274 -0.7774913 -4.025819 1.248671 0.6266133 
+85.00274 -0.7774913 -4.025819 1.248671 0.7310489 
+85.00274 -0.7774913 -4.025819 1.248671 0.6614252 
+85.00274 -0.7774913 -4.025819 1.248671 0.713643 
+85.00274 -0.7774913 -4.025819 1.248671 0.6788311 
+85.00274 -0.7774913 -4.025819 1.248671 0.70494 
+85.00274 -0.7774913 -4.025819 1.248671 0.6875341 
+93.50301 -0.6997422 -4.025819 1.248671 0.696237 
+76.50246 -0.8552405 -4.025819 1.248671 0.696237 
+89.25287 -0.7386168 -4.025819 1.248671 0.696237 
+80.7526 -0.8163659 -4.025819 1.248671 0.696237 
+87.12781 -0.758054 -4.025819 1.248671 0.696237 
+82.87767 -0.7969286 -4.025819 1.248671 0.696237 
+86.06527 -0.7677727 -4.025819 1.248671 0.696237 
+83.9402 -0.78721 -4.025819 1.248671 0.696237 
+93.50301 -0.7774913 -3.623237 1.248671 0.696237 
+76.50246 -0.7774913 -4.428401 1.248671 0.696237 
+89.25287 -0.7774913 -3.824528 1.248671 0.696237 
+80.7526 -0.7774913 -4.22711 1.248671 0.696237 
+87.12781 -0.7774913 -3.925173 1.248671 0.696237 
+82.87767 -0.7774913 -4.126464 1.248671 0.696237 
+86.06527 -0.7774913 -3.975496 1.248671 0.696237 
+83.9402 -0.7774913 -4.076142 1.248671 0.696237 
+85.00274 -0.6997422 -3.623237 1.248671 0.696237 
+85.00274 -0.8552405 -4.428401 1.248671 0.696237 
+85.00274 -0.7386168 -3.824528 1.248671 0.696237 
+85.00274 -0.8163659 -4.22711 1.248671 0.696237 
+85.00274 -0.758054 -3.925173 1.248671 0.696237 
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