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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"> - - - <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" 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href="https://github.com/jranke/mkin/blob/HEAD/R/mkinsub.R" class="external-link"><code>R/mkinsub.R</code></a></small> - <div class="hidden name"><code>mkinmod.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>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 +76,8 @@ 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> @@ -133,15 +90,17 @@ components.</p> <span> overwrite <span class="op">=</span> <span class="cn">FALSE</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mkinmod</span></span> +<span><span class="co"># S3 method for class 'mkinmod'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <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> - <dl><dt>...</dt> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></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 first order kinetics "SFO", indeterminate order rate equation kinetics @@ -158,7 +117,7 @@ fixing the flux to sink to zero. In print.mkinmod, this argument is currently not used.</p></dd> -<dt>use_of_ff</dt> +<dt id="arg-use-of-ff">use_of_ff<a class="anchor" aria-label="anchor" href="#arg-use-of-ff"></a></dt> <dd><p>Specification of the use of formation fractions in the model equations and, if applicable, the coefficient matrix. If "max", formation fractions are always used (default). If "min", a minimum use of @@ -166,26 +125,26 @@ formation fractions is made, i.e. each first-order pathway to a metabolite has its own rate constant.</p></dd> -<dt>name</dt> +<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt> <dd><p>A name for the model. Should be a valid R object name.</p></dd> -<dt>speclist</dt> +<dt id="arg-speclist">speclist<a class="anchor" aria-label="anchor" href="#arg-speclist"></a></dt> <dd><p>The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL.</p></dd> -<dt>quiet</dt> +<dt id="arg-quiet">quiet<a class="anchor" aria-label="anchor" href="#arg-quiet"></a></dt> <dd><p>Should messages be suppressed?</p></dd> -<dt>verbose</dt> +<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if applicable to give detailed information about the C function being built.</p></dd> -<dt>dll_dir</dt> +<dt id="arg-dll-dir">dll_dir<a class="anchor" aria-label="anchor" href="#arg-dll-dir"></a></dt> <dd><p>Directory where an DLL object, if generated internally by <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a permanent location for use in future sessions, if 'dll_dir' and 'name' @@ -194,47 +153,45 @@ as the cache remains functional across sessions if the DLL is stored in a user defined location.</p></dd> -<dt>unload</dt> +<dt id="arg-unload">unload<a class="anchor" aria-label="anchor" href="#arg-unload"></a></dt> <dd><p>If a DLL from the target location in 'dll_dir' is already loaded, should that be unloaded first?</p></dd> -<dt>overwrite</dt> +<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt> <dd><p>If a file exists at the target DLL location in 'dll_dir', should this be overwritten?</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An <code>mkinmod</code> object.</p></dd> -<dt>submodel</dt> +<dt id="arg-submodel">submodel<a class="anchor" aria-label="anchor" href="#arg-submodel"></a></dt> <dd><p>Character vector of length one to specify the submodel type. See <code>mkinmod</code> for the list of allowed submodel names.</p></dd> -<dt>to</dt> +<dt id="arg-to">to<a class="anchor" aria-label="anchor" href="#arg-to"></a></dt> <dd><p>Vector of the names of the state variable to which a transformation shall be included in the model.</p></dd> -<dt>sink</dt> +<dt id="arg-sink">sink<a class="anchor" aria-label="anchor" href="#arg-sink"></a></dt> <dd><p>Should a pathway to sink be included in the model in addition to the pathways to other state variables?</p></dd> -<dt>full_name</dt> +<dt id="arg-full-name">full_name<a class="anchor" aria-label="anchor" href="#arg-full-name"></a></dt> <dd><p>An optional name to be used e.g. for plotting fits performed with the model. You can use non-ASCII characters here, but then 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> - - -<p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, + <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>, containing, among others,</p> <dl><dt>diffs</dt> <dd><p>A vector of string representations of differential equations, one for @@ -262,8 +219,8 @@ 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 +231,14 @@ 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 +247,13 @@ 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 +290,7 @@ 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/RtmpUBdk0y/file210eb9601bdd53.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 +343,7 @@ 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: 0x55555a37aab8></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> @@ -403,27 +360,23 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - 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