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diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html new file mode 100644 index 00000000..daa1ec0b --- /dev/null +++ b/docs/dev/reference/endpoints.html @@ -0,0 +1,181 @@ +<!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, shrink-to-fit=no"><title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints"><meta name="description" content="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."><meta property="og:description" content="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."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" 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href="https://github.com/jranke/mkin/blob/HEAD/R/endpoints.R" class="external-link"><code>R/endpoints.R</code></a></small> + <div class="d-none name"><code>endpoints.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <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 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">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 class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-fit">fit<a class="anchor" aria-label="anchor" href="#arg-fit"></a></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 id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></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 id="arg-covariate-quantile">covariate_quantile<a class="anchor" aria-label="anchor" href="#arg-covariate-quantile"></a></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 class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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 class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></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 class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</p> + </div> + + <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></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> + </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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> + + + + + + </body></html> + |