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<h1>Calculate a time course of relative concentrations based on an mkinmod model</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/pfm_degradation.R" class="external-link"><code>R/pfm_degradation.R</code></a></small>
<div class="d-none name"><code>pfm_degradation.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Calculate a time course of relative concentrations based on an mkinmod model</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">pfm_degradation</span><span class="op">(</span></span>
<span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span>
<span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span>
<span> parms <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>k_parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="va">DT50</span><span class="op">)</span>,</span>
<span> years <span class="op">=</span> <span class="fl">1</span>,</span>
<span> step_days <span class="op">=</span> <span class="fl">1</span>,</span>
<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="va">years</span> <span class="op">*</span> <span class="fl">365</span>, by <span class="op">=</span> <span class="va">step_days</span><span class="op">)</span></span>
<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-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
<dd><p>The degradation model to be used. Either a parent only model like
'SFO' or 'FOMC', or an mkinmod object</p></dd>
<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt>
<dd><p>The half-life. This is only used when simple exponential decline
is calculated (SFO model).</p></dd>
<dt id="arg-parms">parms<a class="anchor" aria-label="anchor" href="#arg-parms"></a></dt>
<dd><p>The parameters used for the degradation model</p></dd>
<dt id="arg-years">years<a class="anchor" aria-label="anchor" href="#arg-years"></a></dt>
<dd><p>For how many years should the degradation be predicted?</p></dd>
<dt id="arg-step-days">step_days<a class="anchor" aria-label="anchor" href="#arg-step-days"></a></dt>
<dd><p>What step size in days should the output have?</p></dd>
<dt id="arg-times">times<a class="anchor" aria-label="anchor" href="#arg-times"></a></dt>
<dd><p>The output times</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A data frame containing the output times and the concentrations
assuming initial concentrations of 1 for the parent and zero for
metabolites, if any.</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 class="co"># Simple example of an SFO decline curve</span></span></span>
<span class="r-in"><span><span class="va">sfo_out</span> <span class="op"><-</span> <span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">sfo_out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> time parent</span>
<span class="r-out co"><span class="r-pr">#></span> 0 0 1.0000000</span>
<span class="r-out co"><span class="r-pr">#></span> 1 1 0.9330330</span>
<span class="r-out co"><span class="r-pr">#></span> 2 2 0.8705506</span>
<span class="r-out co"><span class="r-pr">#></span> 3 3 0.8122524</span>
<span class="r-out co"><span class="r-pr">#></span> 4 4 0.7578583</span>
<span class="r-out co"><span class="r-pr">#></span> 5 5 0.7071068</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Fictive example with a metabolite where we first generate an SFO-SFO model</span></span></span>
<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"metabolite"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> metabolite <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sfo_sfo_out</span> <span class="op"><-</span> <span class="fu">pfm_degradation</span><span class="op">(</span><span class="va">sfo_sfo</span>,</span></span>
<span class="r-in"><span> parms <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>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_metabolite <span class="op">=</span> <span class="fl">0.5</span>, k_metabolite <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"time"</span><span class="op">]</span>,</span></span>
<span class="r-in"><span> <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"parent"</span><span class="op">]</span>, type <span class="op">=</span> <span class="st">"l"</span>,</span></span>
<span class="r-in"><span> xlab <span class="op">=</span> <span class="st">"Time"</span>, ylab <span class="op">=</span> <span class="st">"Relative concentration"</span>,</span></span>
<span class="r-in"><span> xlim <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="fl">0</span>, <span class="fl">100</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/graphics/lines.html" class="external-link">lines</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"time"</span><span class="op">]</span>,</span></span>
<span class="r-in"><span> <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"metabolite"</span><span class="op">]</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="pfm_degradation-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
</code></pre></div>
</div>
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