From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Mon, 15 Feb 2021 17:36:12 +0100
Subject: Fully rebuild docs, rerun tests and check
---
docs/dev/reference/summary.nlme.mmkin.html | 226 ++++++++++++++---------------
1 file changed, 112 insertions(+), 114 deletions(-)
(limited to 'docs/dev/reference/summary.nlme.mmkin.html')
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index 2aeadc46..b2f6624a 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
mkin
- 0.9.50.4
+ 1.0.3.9000
@@ -125,7 +125,7 @@ endpoints such as formation fractions and DT50 values. Optionally
-
-
+
@@ -263,12 +263,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
#> Warning: Optimisation did not converge:
#> iteration limit reached without convergence (10)
#> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
#> nlme version used for fitting: 3.1.150.1
-#> mkin version used for pre-fitting: 0.9.50.4
+
#> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
#> nlme version used for fitting: 3.1.152
+#> mkin version used for pre-fitting: 1.0.3.9000
#> R version used for fitting: 4.0.3
-#> Date of fit: Mon Nov 30 16:01:23 2020
-#> Date of summary: Mon Nov 30 16:01:23 2020
+#> Date of fit: Mon Feb 15 17:13:12 2021
+#> Date of summary: Mon Feb 15 17:13:12 2021
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -278,148 +278,146 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 0.996 s using 6 iterations
+#> Fitted in 0.544 s using 4 iterations
#>
#> Variance model: Two-component variance function
#>
#> Mean of starting values for individual parameters:
#> parent_0 log_k_parent
-#> 101.568773 -4.454103
+#> 101.569 -4.454
#>
#> Fixed degradation parameter values:
#> None
#>
#> Results:
#>
-#> AIC BIC logLik
-#> 586.4159 603.9145 -286.2079
+#> AIC BIC logLik
+#> 584.5 599.5 -286.2
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
#> lower est. upper
-#> parent_0 99.360 101.593 103.825
-#> log_k_parent -4.979 -4.451 -3.924
+#> parent_0 99.371 101.592 103.814
+#> log_k_parent -4.973 -4.449 -3.926
#>
#> Correlation:
#> prnt_0
-#> log_k_parent 0.155
+#> log_k_parent 0.051
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
#> Level: ds
-#> Structure: General positive-definite, Log-Cholesky parametrization
-#> StdDev Corr
-#> parent_0 0.2624248 prnt_0
-#> log_k_parent 0.5907146 0.999
-#> Residual 1.0000000
+#> Structure: Diagonal
+#> parent_0 log_k_parent Residual
+#> StdDev: 6.924e-05 0.5863 1
#>
#> Variance function:
#> Structure: Constant plus proportion of variance covariate
#> Formula: ~fitted(.)
#> Parameter estimates:
-#> const prop
-#> 6.56706e-24 7.89583e-02
+#> const prop
+#> 0.0001208853 0.0789968036
#>
#> Backtransformed parameters with asymmetric confidence intervals:
#> lower est. upper
-#> parent_0 99.360213 101.59280 103.82539
-#> k_parent 0.006883 0.01166 0.01976
+#> parent_0 99.370882 101.59243 103.81398
+#> k_parent 0.006923 0.01168 0.01972
#>
#> Estimated disappearance times:
#> DT50 DT90
-#> parent 59.44 197.4
+#> parent 59.32 197.1
#>
#> Data:
#> ds name time observed predicted residual std standardized
-#> ds 1 parent 0 104.1 101.417 2.68283 8.0077 0.335030
-#> ds 1 parent 0 105.0 101.417 3.58283 8.0077 0.447422
-#> ds 1 parent 1 98.5 100.624 -2.12400 7.9451 -0.267334
-#> ds 1 parent 1 96.1 100.624 -4.52400 7.9451 -0.569407
-#> ds 1 parent 3 101.9 99.056 2.84379 7.8213 0.363595
-#> ds 1 parent 3 85.2 99.056 -13.85621 7.8213 -1.771597
-#> ds 1 parent 7 99.1 95.994 3.10646 7.5795 0.409850
-#> ds 1 parent 7 93.0 95.994 -2.99354 7.5795 -0.394953
-#> ds 1 parent 14 88.1 90.860 -2.75997 7.1741 -0.384710
-#> ds 1 parent 14 84.1 90.860 -6.75997 7.1741 -0.942268
-#> ds 1 parent 28 80.2 81.402 -1.20174 6.4273 -0.186973
-#> ds 1 parent 28 91.3 81.402 9.89826 6.4273 1.540024
-#> ds 1 parent 60 65.1 63.316 1.78361 4.9994 0.356767
-#> ds 1 parent 60 65.8 63.316 2.48361 4.9994 0.496785
-#> ds 1 parent 90 47.8 50.029 -2.22862 3.9502 -0.564182
-#> ds 1 parent 90 53.5 50.029 3.47138 3.9502 0.878792
-#> ds 1 parent 120 37.6 39.529 -1.92946 3.1212 -0.618182
-#> ds 1 parent 120 39.3 39.529 -0.22946 3.1212 -0.073516
-#> ds 2 parent 0 107.9 101.711 6.18875 8.0309 0.770613
-#> ds 2 parent 0 102.1 101.711 0.38875 8.0309 0.048406
-#> ds 2 parent 1 103.8 100.174 3.62597 7.9096 0.458428
-#> ds 2 parent 1 108.6 100.174 8.42597 7.9096 1.065287
-#> ds 2 parent 3 91.0 97.169 -6.16895 7.6723 -0.804055
-#> ds 2 parent 3 84.9 97.169 -12.26895 7.6723 -1.599124
-#> ds 2 parent 7 79.3 91.427 -12.12652 7.2189 -1.679833
-#> ds 2 parent 7 100.9 91.427 9.47348 7.2189 1.312320
-#> ds 2 parent 14 77.3 82.182 -4.88174 6.4889 -0.752318
-#> ds 2 parent 14 83.5 82.182 1.31826 6.4889 0.203155
-#> ds 2 parent 28 66.8 66.402 0.39792 5.2430 0.075895
-#> ds 2 parent 28 63.3 66.402 -3.10208 5.2430 -0.591662
-#> ds 2 parent 60 40.8 40.789 0.01138 3.2206 0.003532
-#> ds 2 parent 60 44.8 40.789 4.01138 3.2206 1.245537
-#> ds 2 parent 90 27.8 25.830 1.97002 2.0395 0.965937
-#> ds 2 parent 90 27.0 25.830 1.17002 2.0395 0.573682
-#> ds 2 parent 120 15.2 16.357 -1.15721 1.2915 -0.895991
-#> ds 2 parent 120 15.5 16.357 -0.85721 1.2915 -0.663710
-#> ds 3 parent 0 97.7 101.907 -4.20726 8.0464 -0.522873
-#> ds 3 parent 0 88.2 101.907 -13.70726 8.0464 -1.703521
-#> ds 3 parent 1 109.9 99.522 10.37805 7.8581 1.320685
-#> ds 3 parent 1 97.8 99.522 -1.72195 7.8581 -0.219130
-#> ds 3 parent 3 100.5 94.918 5.58248 7.4945 0.744875
-#> ds 3 parent 3 77.4 94.918 -17.51752 7.4945 -2.337375
-#> ds 3 parent 7 78.3 86.338 -8.03788 6.8171 -1.179077
-#> ds 3 parent 7 90.3 86.338 3.96212 6.8171 0.581204
-#> ds 3 parent 14 76.0 73.147 2.85281 5.7756 0.493944
-#> ds 3 parent 14 79.1 73.147 5.95281 5.7756 1.030687
-#> ds 3 parent 28 46.0 52.504 -6.50373 4.1456 -1.568826
-#> ds 3 parent 28 53.4 52.504 0.89627 4.1456 0.216197
-#> ds 3 parent 60 25.1 24.605 0.49461 1.9428 0.254586
-#> ds 3 parent 60 21.4 24.605 -3.20539 1.9428 -1.649882
-#> ds 3 parent 90 11.0 12.090 -1.09046 0.9546 -1.142271
-#> ds 3 parent 90 14.2 12.090 2.10954 0.9546 2.209770
-#> ds 3 parent 120 5.8 5.941 -0.14094 0.4691 -0.300464
-#> ds 3 parent 120 6.1 5.941 0.15906 0.4691 0.339077
-#> ds 4 parent 0 95.3 101.177 -5.87672 7.9887 -0.735625
-#> ds 4 parent 0 102.0 101.177 0.82328 7.9887 0.103056
-#> ds 4 parent 1 104.4 100.716 3.68438 7.9523 0.463307
-#> ds 4 parent 1 105.4 100.716 4.68438 7.9523 0.589057
-#> ds 4 parent 3 113.7 99.800 13.90026 7.8800 1.763989
-#> ds 4 parent 3 82.3 99.800 -17.49974 7.8800 -2.220774
-#> ds 4 parent 7 98.1 97.993 0.10713 7.7374 0.013846
-#> ds 4 parent 7 87.8 97.993 -10.19287 7.7374 -1.317359
-#> ds 4 parent 14 97.9 94.909 2.99079 7.4939 0.399098
-#> ds 4 parent 14 104.8 94.909 9.89079 7.4939 1.319851
-#> ds 4 parent 28 85.0 89.030 -4.02995 7.0297 -0.573279
-#> ds 4 parent 28 77.2 89.030 -11.82995 7.0297 -1.682864
-#> ds 4 parent 60 82.2 76.923 5.27690 6.0737 0.868808
-#> ds 4 parent 60 86.1 76.923 9.17690 6.0737 1.510919
-#> ds 4 parent 90 70.5 67.073 3.42743 5.2959 0.647182
-#> ds 4 parent 90 61.7 67.073 -5.37257 5.2959 -1.014470
-#> ds 4 parent 120 60.0 58.483 1.51654 4.6178 0.328416
-#> ds 4 parent 120 56.4 58.483 -2.08346 4.6178 -0.451184
-#> ds 5 parent 0 92.6 101.752 -9.15161 8.0341 -1.139091
-#> ds 5 parent 0 116.5 101.752 14.74839 8.0341 1.835716
-#> ds 5 parent 1 108.0 100.069 7.93112 7.9013 1.003778
-#> ds 5 parent 1 104.9 100.069 4.83112 7.9013 0.611436
-#> ds 5 parent 3 100.5 96.786 3.71355 7.6421 0.485934
-#> ds 5 parent 3 89.5 96.786 -7.28645 7.6421 -0.953462
-#> ds 5 parent 7 91.7 90.541 1.15895 7.1490 0.162114
-#> ds 5 parent 7 95.1 90.541 4.55895 7.1490 0.637707
-#> ds 5 parent 14 82.2 80.566 1.63437 6.3613 0.256923
-#> ds 5 parent 14 84.5 80.566 3.93437 6.3613 0.618483
-#> ds 5 parent 28 60.5 63.791 -3.29084 5.0368 -0.653357
-#> ds 5 parent 28 72.8 63.791 9.00916 5.0368 1.788662
-#> ds 5 parent 60 38.3 37.412 0.88840 2.9540 0.300748
-#> ds 5 parent 60 40.7 37.412 3.28840 2.9540 1.113217
-#> ds 5 parent 90 22.5 22.685 -0.18500 1.7912 -0.103287
-#> ds 5 parent 90 20.8 22.685 -1.88500 1.7912 -1.052387
-#> ds 5 parent 120 13.4 13.755 -0.35534 1.0861 -0.327173
-#> ds 5 parent 120 13.8 13.755 0.04466 1.0861 0.041118
+#> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451
+#> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594
+#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313
+#> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725
+#> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796
+#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812
+#> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081
+#> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065
+#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987
+#> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480
+#> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857
+#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364
+#> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008
+#> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898
+#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252
+#> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335
+#> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423
+#> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549
+#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943
+#> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245
+#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361
+#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626
+#> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297
+#> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874
+#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251
+#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647
+#> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366
+#> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571
+#> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748
+#> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002
+#> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679
+#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485
+#> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198
+#> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171
+#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595
+#> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547
+#> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009
+#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739
+#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858
+#> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921
+#> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603
+#> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360
+#> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813
+#> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620
+#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848
+#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722
+#> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842
+#> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046
+#> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676
+#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664
+#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199
+#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776
+#> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178
+#> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282
+#> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057
+#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784
+#> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025
+#> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205
+#> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218
+#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886
+#> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706
+#> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270
+#> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357
+#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521
+#> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001
+#> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017
+#> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526
+#> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571
+#> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733
+#> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591
+#> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058
+#> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530
+#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485
+#> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531
+#> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413
+#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655
+#> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477
+#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382
+#> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267
+#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304
+#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295
+#> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141
+#> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178
+#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062
+#> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835
+#> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174
+#> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913
+#> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273
+#> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259
+#> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517