diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-04-10 10:17:35 +0200 |
| commit | 194659fcaccdd1ee37851725b8c72e99daa3a8cf (patch) | |
| tree | edbbebe8956000b9eb725ca425b91e051571ec02 /docs/reference/test_data_from_UBA_2014.html | |
| parent | 5814be02f286ce96d6cff8d698aea6844e4025f1 (diff) | |
Adapt tests, vignettes and examples
- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit
Diffstat (limited to 'docs/reference/test_data_from_UBA_2014.html')
| -rw-r--r-- | docs/reference/test_data_from_UBA_2014.html | 70 |
1 files changed, 36 insertions, 34 deletions
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 28e8b41c..dfb49619 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> </span> </div> @@ -158,23 +158,24 @@ <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> <span class='co'># model).</span> <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), - <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_w_0 9.598567e+01 2.33959800 4.102657e+01 9.568967e-19 NA -#> k_parent_w_sink 3.603743e-01 0.03497750 1.030303e+01 4.989002e-09 NA -#> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03 NA -#> k_parent_s_sink 5.108539e-11 0.10382001 4.920572e-10 5.000000e-01 NA -#> k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01 NA -#> Upper -#> parent_w_0 NA -#> k_parent_w_sink NA -#> k_parent_w_parent_s NA -#> k_parent_s_sink NA -#> k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) +#> parent_w_0 9.598567e+01 2.12352039 4.520120e+01 9.476357e-18 +#> k_parent_w_sink 3.603743e-01 0.03149366 1.144276e+01 4.128096e-09 +#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761185e+00 9.436293e-04 +#> k_parent_s_sink 7.560341e-11 0.09483761 7.971881e-10 5.000000e-01 +#> k_parent_s_parent_w 7.419672e-02 0.10738374 6.909493e-01 2.500756e-01 +#> sigma 2.982879e+00 0.50546582 5.901247e+00 1.454824e-05 +#> Lower Upper +#> parent_w_0 91.48420501 100.4871438 +#> k_parent_w_sink 0.30668904 0.4234571 +#> k_parent_w_parent_s 0.03423904 0.1062455 +#> k_parent_s_sink 0.00000000 Inf +#> k_parent_s_parent_w 0.02289956 0.2404043 +#> sigma 2.00184022 3.9639169</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.09246946 5 6 #> parent_w 0.06377096 3 3 -#> parent_s 0.20882324 2 3</div><div class='input'> +#> parent_s 0.20882325 2 3</div><div class='input'> <span class='co'># This is the evaluation used for the validation of software packages</span> <span class='co'># in the expertise from 2014</span> <span class='no'>m_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), @@ -182,27 +183,28 @@ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> - <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773 -#> k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257517 -#> k_M1 0.84258651 0.930121548 0.9058886 1.871938e-01 0.085876516 -#> k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450630 -#> k_M3 0.01122919 0.008044865 1.3958206 8.804912e-02 0.002550984 -#> f_parent_to_M1 0.32240199 0.278620579 1.1571363 1.295467e-01 NA -#> f_parent_to_M2 0.16099854 0.030548888 5.2701931 1.196190e-05 NA -#> f_M1_to_M3 0.27921500 0.314732842 0.8871492 1.920908e-01 0.015016983 -#> f_M2_to_M3 0.55641333 0.650246995 0.8556954 2.004966e-01 0.005360555 + <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_0 76.55425584 0.859186614 89.1008479 1.113866e-26 74.755959751 +#> k_parent 0.12081956 0.004601922 26.2541548 1.077373e-16 0.111561582 +#> k_M1 0.84258651 0.806231481 1.0450925 1.545475e-01 0.113839756 +#> k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013807 +#> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 +#> f_parent_to_M1 0.32240199 0.240803570 1.3388589 9.820821e-02 NA +#> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531225e-05 NA +#> f_M1_to_M3 0.27921500 0.269443517 1.0362654 1.565440e-01 0.022992921 +#> f_M2_to_M3 0.55641333 0.595125456 0.9349513 1.807725e-01 0.008003316 +#> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper -#> parent_0 78.50591790 -#> k_parent 0.13120341 -#> k_M1 8.26712661 -#> k_M2 0.08266188 -#> k_M3 0.04942981 +#> parent_0 78.35255192 +#> k_parent 0.13084582 +#> k_M1 6.23641562 +#> k_M2 0.09843279 +#> k_M3 0.04333950 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.90777163 -#> f_M2_to_M3 0.99658633</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df +#> f_M1_to_M3 0.86443090 +#> f_M2_to_M3 0.99489847 +#> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.09649963 9 20 #> parent 0.04721283 2 6 #> M1 0.26551209 2 5 |