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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
| commit | 8b7edd4eaf0d196e674a085f744d1a69260a6c91 (patch) | |
| tree | 96d79f504b775d2626ab2a9f700732bd142d66d9 /docs/reference/mkinmod.html | |
| parent | 6ae6b5230efd2e3d25b68600bd988ded60d3db77 (diff) | |
Update pkgdown docs to bootstrap 5 with search
Diffstat (limited to 'docs/reference/mkinmod.html')
| -rw-r--r-- | docs/reference/mkinmod.html | 214 |
1 files changed, 90 insertions, 124 deletions
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Print mkinmod objects in a way that the user finds his way to get to its components."><!-- 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"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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<div class="hidden name"><code>mkinmod.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to set up a kinetic model with one or more state variables</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinmod.R" class="external-link"><code>R/mkinmod.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinsub.R" class="external-link"><code>R/mkinsub.R</code></a></small> + <div class="d-none name"><code>mkinmod.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function is usually called using a call to <code>mkinsub()</code> for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples).</p> @@ -120,7 +89,8 @@ variable, specifying the corresponding submodel as well as outgoing pathways components.</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">mkinmod</span><span class="op">(</span></span> <span> <span class="va">...</span>,</span> <span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> @@ -139,8 +109,8 @@ components.</p> <span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>...</dt> <dd><p>For each observed variable, a list as obtained by <code>mkinsub()</code> has to be specified as an argument (see examples). Currently, single @@ -230,8 +200,8 @@ your R code will not be portable, <em>i.e.</em> may produce unintended plot results on other operating systems or system configurations.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, @@ -262,8 +232,8 @@ returned by cfunction.</p></dd> </dl><p>A list for use with <code>mkinmod</code>.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used.</p> <p>For kinetic models with more than one observed variable, a symbolic solution @@ -274,14 +244,14 @@ is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The IORE submodel is not well tested for metabolites. When using this model for metabolites, you may want to read the note in the help page to <a href="mkinfit.html">mkinfit</a>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -290,13 +260,13 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </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></span> <span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> <span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -333,7 +303,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</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-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkUSV6I/file244bcd2ba24b1a.so to /home/agsad.admin.ch/f80868656/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmpjn19MY/filee5f2f55ca8372.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -386,7 +356,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x560630960080></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x555555f44b28></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> @@ -403,26 +373,22 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <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> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <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> + </footer></div> - </body></html> |