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variable, specifying the corresponding submodel as well as outgoing pathways
(see examples).
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-components." />
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@@ -81,8 +26,7 @@ components." />
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+ <ul class="nav navbar-nav"><li>
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@@ -91,8 +35,7 @@ components." />
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+ <ul class="dropdown-menu" role="menu"><li>
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<li>
@@ -116,34 +59,27 @@ components." />
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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<span class="fab fa-github fa-lg"></span>
</a>
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+ </header><div class="row">
<div class="col-md-9 contents">
<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/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>
+ <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="hidden name"><code>mkinmod.Rd</code></div>
</div>
@@ -155,29 +91,29 @@ variable, specifying the corresponding submodel as well as outgoing pathways
components.</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>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><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" class="external-link">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></code></pre></div>
+ </div>
- <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>
+ <div id="arguments">
+ <h2>Arguments</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
first order kinetics "SFO", indeterminate order rate equation kinetics
"IORE", or single first order with reversible binding "SFORB" are
@@ -190,249 +126,234 @@ 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
+In print.mkinmod, this argument is currently not used.</p></dd>
+<dt>use_of_ff</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
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
+has its own rate constant.</p></dd>
+<dt>name</dt>
+<dd><p>A name for the model. Should be a valid R object name.</p></dd>
+<dt>speclist</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></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
+argument. Default is NULL.</p></dd>
+<dt>quiet</dt>
+<dd><p>Should messages be suppressed?</p></dd>
+<dt>verbose</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>
+<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'
-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
+are specified.</p></dd>
+<dt>unload</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>
+<dd><p>If a file exists at the target DLL location in 'dll_dir',
+should this be overwritten?</p></dd>
+<dt>x</dt>
+<dd><p>An <code>mkinmod</code> object.</p></dd>
+<dt>submodel</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>
+<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>
+<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>
+<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></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>,
+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>,
containing, among others,</p>
-<dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for
+<dl><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,
+<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
+<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
+<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
+<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>
-
+</dl><p>A list for use with <code>mkinmod</code>.</p>
+ </div>
+ <div id="details">
+ <h2>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
+<p>If a C compiler is found by <code><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html" class="external-link">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>
-
+<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>
<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) &#8220;Guidance Document on Estimating Persistence
+page to <a href="mkinfit.html">mkinfit</a>.</p>
+ </div>
+ <div id="references">
+ <h2>References</h2>
+ <p>FOCUS (2006) “Guidance Document on Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+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>
+<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">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>
-
+ </div>
+ <div id="author">
+ <h2>Author</h2>
<p>Johannes Ranke</p>
+ </div>
- <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'>&lt;-</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'>&lt;-</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'>#&gt; <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'>#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: max
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $to: m1; $sink: TRUE
-#&gt; $m1
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Compiled model $cf available
-#&gt; Differential equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; 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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>&lt;-</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'>#&gt; <span class='message'>Copied DLL from /tmp/RtmpWsX48Z/file1029f864aada00.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'>&lt;-</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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; Program source:
-#&gt; 1: #include &lt;R.h&gt;
-#&gt; 2:
-#&gt; 3:
-#&gt; 4: static double parms [3];
-#&gt; 5: #define k_parent parms[0]
-#&gt; 6: #define f_parent_to_m1 parms[1]
-#&gt; 7: #define k_m1 parms[2]
-#&gt; 8:
-#&gt; 9: void initpar(void (* odeparms)(int *, double *)) {
-#&gt; 10: int N = 3;
-#&gt; 11: odeparms(&amp;N, parms);
-#&gt; 12: }
-#&gt; 13:
-#&gt; 14:
-#&gt; 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
-#&gt; 16:
-#&gt; 17: f[0] = - k_parent * y[0];
-#&gt; 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
-#&gt; 19: }</div><div class='output co'>#&gt; <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'>#&gt; function (observed, odeini, odeparms)
-#&gt; {
-#&gt; predicted &lt;- numeric(0)
-#&gt; with(as.list(odeparms), {
-#&gt; t &lt;- observed[observed$name == "parent", "time"]
-#&gt; predicted &lt;&lt;- c(predicted, SFO.solution(t, odeini["parent"],
-#&gt; k_parent))
-#&gt; t &lt;- observed[observed$name == "m1", "time"]
-#&gt; predicted &lt;&lt;- c(predicted, (((k_m1 - k_parent) * odeini["m1"] -
-#&gt; f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 *
-#&gt; t) + f_parent_to_m1 * k_parent * odeini["parent"] *
-#&gt; exp(-k_parent * t))/(k_m1 - k_parent))
-#&gt; })
-#&gt; return(predicted)
-#&gt; }
-#&gt; &lt;environment: 0x55555cc38878&gt;</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'>&lt;-</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'>&lt;-</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>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
+<span class="r-in"><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span>
+<span class="r-in"><span class="va">SFO</span> <span class="op">&lt;-</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 class="r-in"></span>
+<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order</span></span>
+<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
+<span class="r-in"> 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>,</span>
+<span class="r-in"> 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></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><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">SFO_SFO</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mkinmod&gt; model generated with</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Use of formation fractions $use_of_ff: max </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Specification $spec:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $parent</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $type: SFO; $to: m1; $sink: TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $m1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $type: SFO; $sink: TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Coefficient matrix $coefmat available</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Compiled model $cf available</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Differential equations:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op">&lt;-</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></span>
+<span class="r-in"></span>
+<span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span>
+<span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span>
+<span class="r-in"> <span class="va">DLL_dir</span> <span class="op">&lt;-</span> <span class="st">"~/.local/share/mkin"</span></span>
+<span class="r-in"> <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" class="external-link">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" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span>
+<span class="r-in"> <span class="va">SFO_SFO.2</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
+<span class="r-in"> 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>,</span>
+<span class="r-in"> 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 class="r-in"> 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 class="r-msg co"><span class="r-pr">#&gt;</span> Copied DLL from /tmp/Rtmp6NiOcv/fileb89c01ace19ec.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span>
+<span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span>
+<span class="r-in"><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 class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span>
+<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">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>
+<span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op">&lt;-</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></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># Show details of creating the C function</span></span>
+<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
+<span class="r-in"> 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>,</span>
+<span class="r-in"> 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></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Program source:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1: #include &lt;R.h&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4: static double parms [3];</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5: #define k_parent parms[0]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6: #define f_parent_to_m1 parms[1]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7: #define k_m1 parms[2]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9: void initpar(void (* odeparms)(int *, double *)) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10: int N = 3;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11: odeparms(&amp;N, parms);</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12: }</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 16: </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 17: f[0] = - k_parent * y[0];</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 19: }</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># The symbolic solution which is available in this case is not</span></span>
+<span class="r-in"><span class="co"># made for human reading but for speed of computation</span></span>
+<span class="r-in"><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> function (observed, odeini, odeparms) </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> predicted &lt;- numeric(0)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> with(as.list(odeparms), {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> t &lt;- observed[observed$name == "parent", "time"]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> predicted &lt;&lt;- c(predicted, SFO.solution(t, odeini["parent"], </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> t &lt;- observed[observed$name == "m1", "time"]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> predicted &lt;&lt;- c(predicted, (((k_m1 - k_parent) * odeini["m1"] - </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 * </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> t) + f_parent_to_m1 * k_parent * odeini["parent"] * </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> exp(-k_parent * t))/(k_m1 - k_parent))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> return(predicted)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55555cd83c70&gt;</span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># If we have several parallel metabolites</span></span>
+<span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span>
+<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
+<span class="r-in"> 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" class="external-link">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>,</span>
+<span class="r-in"> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span class="r-in"> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">fit_DFOP_par_c</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span>
+<span class="r-in"> <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>,</span>
+<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span class="co"># }</span></span>
+<span class="r-in"></span>
+</code></pre></div>
+ </div>
</div>
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