aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/parms.html
blob: 18f3566ec6bf10a3e0d985c54d975252ef9cf33b (plain) (tree)
1
2
3
4
5
6
7
8
9
               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                               
                                                              
 
                                                    
                                                                                    








                                                                                                                               
                                                                                                                                     


                                                      
                                     

                                                          
                                                                                                                           


                               
                                            







                                                                                                 

                                                                                                                                                      









                                                                                                                             

                                                                               
            

                                       
                                                                  
                                             

      
                                       



                           
                                

                                                         
                                                                                                                                                                           







                                                                                 
                                                                                                                                                                                                      
 
                                                                                                                                                                                                               
 

                                                                                                                                                                                                                                  
 











                                                                                                                                 


                                                                          
          
 




































                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                   
                                                                                   
                                                                                   
















                                                                                                                                     
                                                                                                                                    
                                                                                                                                    
                                                                                                                                    

























                                                                                                                                                                                                         
        
                                                                 
                                                                                      

      
                                            

                     
                                                                                                             
      
                     


  
  
 
                
 
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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."><!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</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/" class="external-link">
    <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/HEAD/R/parms.mkinfit.R" class="external-link"><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>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><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></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>object</dt>
<dd><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></dd>
<dt>...</dt>
<dd><p>Not used</p></dd>
<dt>transformed</dt>
<dd><p>Should the parameters be returned
as used internally during the optimisation?</p></dd>
</dl></div>
    <div id="value">
    <h2>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>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># mkinfit objects</span></span>
<span class="r-in"><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>
<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   parent_0   k_parent      sigma </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 82.4921598  0.3060633  4.6730124 </span>
<span class="r-in"><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></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     parent_0 log_k_parent        sigma </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    82.492160    -1.183963     4.673012 </span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># mmkin objects</span></span>
<span class="r-in"><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">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>
<span class="r-in"> <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" class="external-link">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" class="external-link">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>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">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" class="external-link">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>
<span class="r-in"><span class="co"># \dontrun{</span></span>
<span class="r-in"><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" class="external-link">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>
<span class="r-in"><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></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     5.15274487  7.040168584  3.6769645  6.4669234  6.50457673</span>
<span class="r-in"><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></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             Dataset 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 82.666781678</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent  0.009647805</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     7.040168584</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>           Dataset 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 92.6837649</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> alpha     0.4967832</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> beta     14.1451255</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     1.9167519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             Dataset 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 91.058971599</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k1        0.044946770</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k2        0.002868336</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g         0.526942414</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     2.221302196</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     5.15274487  7.040168584  3.6769645  6.4669234  6.50457673</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>          Dataset 6  Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> alpha     1.338667  0.4967832  1.639099  1.074460  0.2805272</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> beta     13.033315 14.1451255  5.007077  4.397126  6.9052224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     1.847671  1.9167519  1.066063  3.146056  1.6222778</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            Dataset 6    Dataset 7   Dataset 8   Dataset 9   Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.55213663 91.058971599 90.34509493 98.14858821 94.311323732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k1        0.21954588  0.044946770  0.41232288  0.31697588  0.080663857</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k2        0.02957934  0.002868336  0.07581766  0.03260384  0.003425417</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g         0.44845068  0.526942414  0.66091967  0.65322767  0.342652880</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     1.35690468  2.221302196  1.34169076  2.87159846  1.942067831</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><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></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $SFO</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>              Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     88.522754 82.666782 86.854731 91.777931  82.148094</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737  -4.933090</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma         5.152745  7.040169  3.676964  6.466923   6.504577</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $FOMC</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            Dataset 6  Dataset 7  Dataset 8   Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0  95.5585751 92.6837649 90.7197870 98.38393897  94.848146</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_alpha  0.2916741 -0.6996015  0.4941466  0.07181816  -1.271085</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_beta   2.5675088  2.6493701  1.6108523  1.48095106   1.932278</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma      1.8476712  1.9167519  1.0660627  3.14605557   1.622278</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>           Dataset 6  Dataset 7  Dataset 8  Dataset 9 Dataset 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1   -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2   -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis -0.2069326  0.1078741  0.6673953  0.6332573 -0.6514943</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma     1.3569047  2.2213022  1.3416908  2.8715985  1.9420678</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span class="co"># }</span></span>
</code></pre></div>
    </div>
  </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></p><p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
</div>

      </footer></div>

  


  

  </body></html>

Contact - Imprint