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If the SFORB model was specified -for one of the parents or metabolites, the Eigenvalues are returned. These -are equivalent to the rate constants of the DFOP model, but with the -advantage that the SFORB model can also be used for metabolites."><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">1.2.3</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</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 class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</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 class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</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/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</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> - </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>Function to calculate endpoints for further use from kinetic models fitted -with mkinfit</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/endpoints.R" class="external-link"><code>R/endpoints.R</code></a></small> - <div class="hidden name"><code>endpoints.Rd</code></div> - </div> - - <div class="ref-description"> - <p>This function calculates DT50 and DT90 values as well as formation fractions -from kinetic models fitted with mkinfit. If the SFORB model was specified -for one of the parents or metabolites, the Eigenvalues are returned. These -are equivalent to the rate constants of the DFOP model, but with the -advantage that the SFORB model can also be used for metabolites.</p> - </div> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, covariate_quantile <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>fit</dt> -<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, or -another object that has list components mkinmod containing an <a href="mkinmod.html">mkinmod</a> -degradation model, and two numeric vectors, bparms.optim and bparms.fixed, -that contain parameter values for that model.</p></dd> - - -<dt>covariates</dt> -<dd><p>Numeric vector with covariate values for all variables in -any covariate models in the object. If given, it overrides 'covariate_quantile'.</p></dd> - - -<dt>covariate_quantile</dt> -<dd><p>This argument only has an effect if the fitted -object has covariate models. If so, the default is to show endpoints -for the median of the covariate values (50th percentile).</p></dd> - -</dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>A list with a matrix of dissipation times named distimes, and, if -applicable, a vector of formation fractions named ff and, if the SFORB model -was in use, a vector of eigenvalues of these SFORB models, equivalent to -DFOP rate constants</p> - </div> - <div id="details"> - <h2>Details</h2> - <p>Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from -HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> - </div> - <div id="note"> - <h2>Note</h2> - <p>The function is used internally by <a href="summary.mkinfit.html">summary.mkinfit</a>, -<a href="summary.nlme.mmkin.html">summary.nlme.mmkin</a> and <a href="summary.saem.mmkin.html">summary.saem.mmkin</a>.</p> - </div> - <div id="author"> - <h2>Author</h2> - <p>Johannes Ranke</p> - </div> - - <div id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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">"FOMC"</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">endpoints</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">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back</span> -<span class="r-out co"><span class="r-pr">#></span> parent 1.785233 15.1479 4.559973</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span> <span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</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">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 1.886925 21.25106 6.397207 1.508293 38.83438</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span> <span class="va">fit_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</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">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> $ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_free </span> -<span class="r-out co"><span class="r-pr">#></span> 1 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> $SFORB</span> -<span class="r-out co"><span class="r-pr">#></span> parent_b1 parent_b2 parent_g </span> -<span class="r-out co"><span class="r-pr">#></span> 0.4595574 0.0178488 0.8539454 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_parent_b1 DT50_parent_b2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 1.886925 21.25106 6.397208 1.508293 38.83438</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span> <span class="co"># }</span></span></span> -<span class="r-in"><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> - - - <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> 2.0.7.</p> -</div> - - </footer></div> - - - - - - - </body></html> - |