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<!DOCTYPE html>
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    <div class="page-header">
    <h1>Extract model parameters</h1>
    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.R" class="external-link"><code>R/parms.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small>
    <div class="hidden name"><code>parms.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function returns degradation model parameters as well as error
model parameters per default, 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><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mkinfit</span></span>
<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>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mmkin</span></span>
<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>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for multistart</span></span>
<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, exclude_failed <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for saem.mmkin</span></span>
<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>object</dt>
<dd><p>A fitted model object.</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>


<dt>errparms</dt>
<dd><p>Should the error model parameters be returned
in addition to the degradation parameters?</p></dd>


<dt>exclude_failed</dt>
<dd><p>For <a href="multistart.html">multistart</a> objects, should rows for failed fits
be removed from the returned parameter matrix?</p></dd>


<dt>ci</dt>
<dd><p>Should a matrix with estimates and confidence interval boundaries
be returned? If FALSE (default), a vector of estimates is returned if no
covariates are given, otherwise a matrix of estimates is returned, with
each column corresponding to a row of the data frame holding the covariates</p></dd>


<dt>covariates</dt>
<dd><p>A data frame holding covariate values for which to
return parameter values. Only has an effect if 'ci' is FALSE.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>Depending on the object, a numeric vector of fitted model parameters,
a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for
mmkin objects with more than one row).</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span>
<span class="r-in"><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></span>
<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></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><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>
<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></span>
<span class="r-in"><span><span class="co"># mmkin objects</span></span></span>
<span class="r-in"><span><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>
<span class="r-in"><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" 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>
<span class="r-in"><span><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>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><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" 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>
<span class="r-in"><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></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><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>
<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 91.058971584</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><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></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 94.8481458</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 91.058971584 90.34509493 98.14858820 94.311323735</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><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>
<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  82.148095</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 98.38393898  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><span class="co"># }</span></span></span>
</code></pre></div>
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