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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/parms.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/parms.html')
| -rw-r--r-- | docs/dev/reference/parms.html | 292 |
1 files changed, 292 insertions, 0 deletions
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class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Extract model parameters from mkinfit models</h1> + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small> + <div class="hidden name"><code>parms.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function always returns degradation model parameters as well as error +model parameters, in order to avoid working with a fitted model without +considering the error structure that was assumed for the fit.</p> + </div> + + <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mmkin</span> +<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>A fitted model object. Methods are implemented for +<code><a href='mkinfit.html'>mkinfit()</a></code> objects and for <code><a href='mmkin.html'>mmkin()</a></code> objects.</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used</p></td> + </tr> + <tr> + <th>transformed</th> + <td><p>Should the parameters be returned +as used internally during the optimisation?</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>For mkinfit objects, a numeric vector of fitted model parameters. +For mmkin row objects, a matrix with the parameters with a +row for each dataset. If the mmkin object has more than one row, a list of +such matrices is returned.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># mkinfit objects</span> +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>parms</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent_sink sigma +#> 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink sigma +#> 82.492160 -1.183963 4.673012 </div><div class='input'> +<span class='co'># mmkin objects</span> +<span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], + <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])) +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>) +<span class='co'># \dontrun{</span> +<span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='fu'>parms</span>(<span class='no'>fits</span>[<span class='st'>"SFO"</span>, ])</div><div class='output co'>#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 +#> k_parent_sink 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 +#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>[, <span class='fl'>2</span>])</div><div class='output co'>#> $SFO +#> Dataset 7 +#> parent_0 82.666781678 +#> k_parent_sink 0.009647805 +#> sigma 7.040168584 +#> +#> $FOMC +#> Dataset 7 +#> parent_0 92.6837649 +#> alpha 0.4967832 +#> beta 14.1451255 +#> sigma 1.9167519 +#> +#> $DFOP +#> Dataset 7 +#> parent_0 91.058971503 +#> k1 0.044946770 +#> k2 0.002868336 +#> g 0.526942415 +#> sigma 2.221302196 +#> </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>)</div><div class='output co'>#> $SFO +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 +#> k_parent_sink 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 +#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673 +#> +#> $FOMC +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458 +#> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 +#> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 +#> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 +#> +#> $DFOP +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 96.55213663 91.058971503 90.34509469 98.14858850 94.311323409 +#> k1 0.21954589 0.044946770 0.41232289 0.31697588 0.080663853 +#> k2 0.02957934 0.002868336 0.07581767 0.03260384 0.003425417 +#> g 0.44845068 0.526942415 0.66091965 0.65322767 0.342652880 +#> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 +#> </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> $SFO +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094 +#> log_k_parent_sink -2.848234 -4.641025 -1.559232 -2.093737 -4.933090 +#> sigma 5.152745 7.040169 3.676964 6.466923 6.504577 +#> +#> $FOMC +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 95.5585751 92.6837649 90.7197870 98.38393896 94.848146 +#> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181817 -1.271085 +#> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278 +#> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278 +#> +#> $DFOP +#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 +#> parent_0 96.5521366 91.05897150 90.3450947 98.1485885 94.311323 +#> log_k1 -1.5161940 -3.10227638 -0.8859485 -1.1489296 -2.517465 +#> log_k2 -3.5206791 -5.85402317 -2.5794240 -3.4233253 -5.676532 +#> g_ilr -0.1463234 0.07627854 0.4719196 0.4477805 -0.460676 +#> sigma 1.3569047 2.22130220 1.3416908 2.8715985 1.942068 +#> </div><div class='input'># } +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |