aboutsummaryrefslogblamecommitdiff
path: root/docs/dev/reference/parms.html
blob: 9f6f4225049c15d301c7cbb1b60446d56e26aef6 (plain) (tree)










































































                                                                                                                                                                                                             
                                                                                                                                             













































                                                                                                                             
                                            
                                             















                                                         
                                                                                                                                                       







                                                                                 
                                                                                                                                                                 
                                               
                                                                                                                                                                                                               
                                             
                                                                                                                                                                                                                     



























                                                                                                                                 



                                                                                                                                                                                                                                                                                                       
                                                                      
                                       

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                   

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                         
                                                                                                                                                                                                                                                                                          


                           








                           
                           
                           
                           
                           
                                                                                                                                          


                                                                         

                                                                  
                                                                  




                                                                            
                                                                            
                                                                            
                                                                            
                                                                            
                                                                                                                                                                                                              


                                                                     

                                                                       
                                                                       


                                                                       





                                                                     














                                                                 
                                                                                










               
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
  <head>
  <meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>Extract model parameters from mkinfit models — parms • mkin</title>


<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />

<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>

<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>

<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>

<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>




<meta property="og:title" content="Extract model parameters from mkinfit models — parms" />
<meta property="og:description" content="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." />


<meta name="robots" content="noindex">

<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>

<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->



  </head>

  <body data-spy="scroll" data-target="#toc">
    <div class="container template-reference-topic">
      <header>
      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </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">1.0.3.9000</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="https://github.com/jranke/mkin/">
    <span class="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='https://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='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span>

<span class='co'># S3 method for mkinfit</span>
<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>

<span class='co'># S3 method for mmkin</span>
<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</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='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='output co'>#&gt;   parent_0   k_parent      sigma 
#&gt; 82.4921598  0.3060633  4.6730124 </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt;     parent_0 log_k_parent        sigma 
#&gt;    82.492160    -1.183963     4.673012 </div><div class='input'>
<span class='co'># mmkin objects</span>
<span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
 <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
<span class='co'># \dontrun{</span>
<span class='va'>fits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt;            Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10
#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
#&gt; k_parent  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421
#&gt; sigma     5.15274487  7.040168584  3.6769645  6.4669234  6.50457673</div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $SFO
#&gt;             Dataset 7
#&gt; parent_0 82.666781678
#&gt; k_parent  0.009647805
#&gt; sigma     7.040168584
#&gt; 
#&gt; $FOMC
#&gt;           Dataset 7
#&gt; parent_0 92.6837649
#&gt; alpha     0.4967832
#&gt; beta     14.1451255
#&gt; sigma     1.9167519
#&gt; 
#&gt; $DFOP
#&gt;             Dataset 7
#&gt; parent_0 91.058971589
#&gt; k1        0.044946770
#&gt; k2        0.002868336
#&gt; g         0.526942415
#&gt; sigma     2.221302196
#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $SFO
#&gt;            Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10
#&gt; parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
#&gt; k_parent  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421
#&gt; sigma     5.15274487  7.040168584  3.6769645  6.4669234  6.50457673
#&gt; 
#&gt; $FOMC
#&gt;          Dataset 6  Dataset 7 Dataset 8 Dataset 9 Dataset 10
#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459
#&gt; alpha     1.338667  0.4967832  1.639099  1.074460  0.2805272
#&gt; beta     13.033315 14.1451255  5.007077  4.397126  6.9052224
#&gt; sigma     1.847671  1.9167519  1.066063  3.146056  1.6222778
#&gt; 
#&gt; $DFOP
#&gt;            Dataset 6    Dataset 7   Dataset 8   Dataset 9   Dataset 10
#&gt; parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734
#&gt; k1        0.21954588  0.044946770  0.41232288  0.31697588  0.080663857
#&gt; k2        0.02957934  0.002868336  0.07581766  0.03260384  0.003425417
#&gt; g         0.44845068  0.526942415  0.66091967  0.65322767  0.342652880
#&gt; sigma     1.35690468  2.221302196  1.34169076  2.87159846  1.942067831
#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $SFO
#&gt;              Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
#&gt; parent_0     88.522754 82.666782 86.854731 91.777931  82.148094
#&gt; log_k_parent -2.848234 -4.641025 -1.559232 -2.093737  -4.933090
#&gt; sigma         5.152745  7.040169  3.676964  6.466923   6.504577
#&gt; 
#&gt; $FOMC
#&gt;            Dataset 6  Dataset 7  Dataset 8   Dataset 9 Dataset 10
#&gt; parent_0  95.5585751 92.6837649 90.7197870 98.38393897  94.848146
#&gt; log_alpha  0.2916741 -0.6996015  0.4941466  0.07181816  -1.271085
#&gt; log_beta   2.5675088  2.6493701  1.6108523  1.48095106   1.932278
#&gt; sigma      1.8476712  1.9167519  1.0660627  3.14605557   1.622278
#&gt; 
#&gt; $DFOP
#&gt;           Dataset 6  Dataset 7  Dataset 8  Dataset 9 Dataset 10
#&gt; parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237
#&gt; log_k1   -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647
#&gt; log_k2   -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322
#&gt; g_qlogis -0.2069326  0.1078741  0.6673953  0.6332573 -0.6514943
#&gt; sigma     1.3569047  2.2213022  1.3416908  2.8715985  1.9420678
#&gt; </div><div class='input'><span class='co'># }</span>
</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> 1.6.1.</p>
</div>

      </footer>
   </div>

  


  </body>
</html>


Contact - Imprint