diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
| commit | b9be19af5e3085216d0cd5af439332f631fa8b92 (patch) | |
| tree | e10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs/dev/reference/summary.nlme.mmkin.html | |
| parent | 11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff) | |
Fully rebuild docs, rerun tests and check
Diffstat (limited to 'docs/dev/reference/summary.nlme.mmkin.html')
| -rw-r--r-- | docs/dev/reference/summary.nlme.mmkin.html | 226 |
1 files changed, 112 insertions, 114 deletions
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 </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -125,7 +125,7 @@ endpoints such as formation fractions and DT50 values. Optionally <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -263,12 +263,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> #> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> nlme version used for fitting: 3.1.150.1 -#> mkin version used for pre-fitting: 0.9.50.4 +</div><div class='output co'>#> <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> 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</p> #> #> 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</div><div class='input'> +#> 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</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |