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<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/master/R/mkinmod.R'><code>R/mkinmod.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small>
<div class="hidden name"><code>mkinmod.Rd</code></div>
</div>
<div class="ref-description">
<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>
<p>Print mkinmod objects in a way that the user finds his way to get to its
components.</p>
<p>This is a convenience function to set up the lists used as arguments for
<code>mkinmod</code>.</p>
</div>
<pre class="usage"><span class='fu'>mkinmod</span><span class='op'>(</span>
<span class='va'>...</span>,
use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>,
name <span class='op'>=</span> <span class='cn'>NULL</span>,
speclist <span class='op'>=</span> <span class='cn'>NULL</span>,
quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
dll_dir <span class='op'>=</span> <span class='cn'>NULL</span>,
unload <span class='op'>=</span> <span class='cn'>FALSE</span>,
overwrite <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span>
<span class='co'># S3 method for mkinmod</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</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></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><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
"IORE", or single first order with reversible binding "SFORB" are
implemented for all variables, while "FOMC", "DFOP", "HS" and "logistic"
can additionally be chosen for the first variable which is assumed to be
the source compartment.
Additionally, <code>mkinsub()</code> has an argument <code>to</code>, specifying names of
variables to which a transfer is to be assumed in the model.
If the argument <code>use_of_ff</code> is set to "min"
(default) and the model for the compartment is "SFO" or "SFORB", an
additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively
fixing the flux to sink to zero.
In print.mkinmod, this argument is currently not used.</p></td>
</tr>
<tr>
<th>use_of_ff</th>
<td><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
formation fractions is made, i.e. each first-order pathway to a metabolite
has its own rate constant.</p></td>
</tr>
<tr>
<th>name</th>
<td><p>A name for the model. Should be a valid R object name.</p></td>
</tr>
<tr>
<th>speclist</th>
<td><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></td>
</tr>
<tr>
<th>quiet</th>
<td><p>Should messages be suppressed?</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>If <code>TRUE</code>, passed to <code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></code> if
applicable to give detailed information about the C function being built.</p></td>
</tr>
<tr>
<th>dll_dir</th>
<td><p>Directory where an DLL object, if generated internally by
<code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>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'
are specified.</p></td>
</tr>
<tr>
<th>unload</th>
<td><p>If a DLL from the target location in 'dll_dir' is already
loaded, should that be unloaded first?</p></td>
</tr>
<tr>
<th>overwrite</th>
<td><p>If a file exists at the target DLL location in 'dll_dir',
should this be overwritten?</p></td>
</tr>
<tr>
<th>x</th>
<td><p>An <code>mkinmod</code> object.</p></td>
</tr>
<tr>
<th>submodel</th>
<td><p>Character vector of length one to specify the submodel type.
See <code>mkinmod</code> for the list of allowed submodel names.</p></td>
</tr>
<tr>
<th>to</th>
<td><p>Vector of the names of the state variable to which a
transformation shall be included in the model.</p></td>
</tr>
<tr>
<th>sink</th>
<td><p>Should a pathway to sink be included in the model in addition to
the pathways to other state variables?</p></td>
</tr>
<tr>
<th>full_name</th>
<td><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></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit()</a></code>,
containing, among others,</p>
<dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for
each modelling variable.</p></dd>
<dt>map</dt><dd><p>A list containing named character vectors for each observed variable,
specifying the modelling variables by which it is represented.</p></dd>
<dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
<dt>deg_func</dt><dd><p>If generated, a function containing the solution of the degradation
model.</p></dd>
<dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be
represented by one.</p></dd>
<dt>cf</dt><dd><p>If generated, a compiled function calculating the derivatives as
returned by cfunction.</p></dd>
A list for use with mkinmod.
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</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
of the system of differential equations is included in the resulting
mkinmod object in some cases, speeding up the solution.</p>
<p>If a C compiler is found by <code><a href='https://rdrr.io/pkg/pkgbuild/man/has_compiler.html'>pkgbuild::has_compiler()</a></code> and there
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'>inline::cfunction()</a></code> and added to the resulting mkinmod object.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</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>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</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,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Johannes Ranke</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'>
<span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</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 class='co'># One parent compound, one metabolite, both single first order</span>
<span class='va'>SFO_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='st'>"m1"</span><span class='op'>)</span>,
m1 <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>
</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span><span class='op'>)</span>
</div><div class='output co'>#> <mkinmod> model generated with
#> Use of formation fractions $use_of_ff: max
#> Specification $spec:
#> $parent
#> $type: SFO; $to: m1; $sink: TRUE
#> $m1
#> $type: SFO; $sink: TRUE
#> Coefficient matrix $coefmat available
#> Compiled model $cf available
#> Differential equations:
#> d_parent/dt = - k_parent * parent
#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='va'>fit_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
<span class='co'># Now supplying compound names used for plotting, and write to user defined location</span>
<span class='co'># We need to choose a path outside the session tempdir because this gets removed</span>
<span class='va'>DLL_dir</span> <span class='op'><-</span> <span class='st'>"~/.local/share/mkin"</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.exists</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/files2.html'>dir.create</a></span><span class='op'>(</span><span class='va'>DLL_dir</span><span class='op'>)</span>
<span class='va'>SFO_SFO.2</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='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</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>,
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>
</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/RtmpkoTT3P/filecc29e29e1b974.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
<span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>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 class='co'># Terminate the R session here if you would like to check, and then do</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
<span class='va'>SFO_SFO.3</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>readRDS</a></span><span class='op'>(</span><span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
<span class='va'>fit_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.3</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
<span class='co'># Show details of creating the C function</span>
<span class='va'>SFO_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='st'>"m1"</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#> Program source:
#> 1: #include <R.h>
#> 2:
#> 3:
#> 4: static double parms [3];
#> 5: #define k_parent parms[0]
#> 6: #define f_parent_to_m1 parms[1]
#> 7: #define k_m1 parms[2]
#> 8:
#> 9: void initpar(void (* odeparms)(int *, double *)) {
#> 10: int N = 3;
#> 11: odeparms(&N, parms);
#> 12: }
#> 13:
#> 14:
#> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
#> 16:
#> 17: f[0] = - k_parent * y[0];
#> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
#> 19: }</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
<span class='co'># The symbolic solution which is available in this case is not</span>
<span class='co'># made for human reading but for speed of computation</span>
<span class='va'>SFO_SFO</span><span class='op'>$</span><span class='va'>deg_func</span>
</div><div class='output co'>#> function (observed, odeini, odeparms)
#> {
#> predicted <- numeric(0)
#> with(as.list(odeparms), {
#> t <- observed[observed$name == "parent", "time"]
#> predicted <<- c(predicted, SFO.solution(t, odeini["parent"],
#> k_parent))
#> t <- observed[observed$name == "m1", "time"]
#> predicted <<- c(predicted, (((k_m1 - k_parent) * odeini["m1"] -
#> f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 *
#> t) + f_parent_to_m1 * k_parent * odeini["parent"] *
#> exp(-k_parent * t))/(k_m1 - k_parent))
#> })
#> return(predicted)
#> }
#> <environment: 0x55555a57f6c8></div><div class='input'>
<span class='co'># If we have several parallel metabolites</span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='va'>m_synth_DFOP_par</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'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
M1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
M2 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>fit_DFOP_par_c</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>,
<span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>,
quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='co'># }</span>
</div></pre>
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