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<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</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> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><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="d-none name"><code>parms.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <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="co"># S3 method for class '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="co"># S3 method for class '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="co"># S3 method for class '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="co"># S3 method for class '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> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>A fitted model object.</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Not used</p></dd> -<dt>transformed</dt> +<dt id="arg-transformed">transformed<a class="anchor" aria-label="anchor" href="#arg-transformed"></a></dt> <dd><p>Should the parameters be returned as used internally during the optimisation?</p></dd> -<dt>errparms</dt> +<dt id="arg-errparms">errparms<a class="anchor" aria-label="anchor" href="#arg-errparms"></a></dt> <dd><p>Should the error model parameters be returned in addition to the degradation parameters?</p></dd> -<dt>exclude_failed</dt> +<dt id="arg-exclude-failed">exclude_failed<a class="anchor" aria-label="anchor" href="#arg-exclude-failed"></a></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> +<dt id="arg-ci">ci<a class="anchor" aria-label="anchor" href="#arg-ci"></a></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> +<dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></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, + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></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="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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"><-</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> @@ -217,10 +175,10 @@ mmkin objects with more than one row).</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971584</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942414</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> <span class="r-out co"><span class="r-pr">#></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> @@ -232,29 +190,29 @@ mmkin objects with more than one row).</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $FOMC</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458</span> <span class="r-out co"><span class="r-pr">#></span> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272</span> <span class="r-out co"><span class="r-pr">#></span> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971584 90.34509493 98.14858820 94.311323735</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> <span class="r-out co"><span class="r-pr">#></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">#></span> $SFO</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148095</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.152745 7.040169 3.676964 6.466923 6.504577</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $FOMC</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393898 94.848146</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278</span> @@ -270,27 +228,23 @@ mmkin objects with more than one row).</p> <span class="r-in"><span><span class="co"># }</span></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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <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> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer></div> + </footer></div> + - - </body></html> |