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-rw-r--r--docs/dev/reference/mkinmod.html199
1 files changed, 123 insertions, 76 deletions
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 5d362f76..145dee83 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
</span>
</div>
@@ -30,7 +30,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
<a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
@@ -45,19 +45,28 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
<li>
- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
</ul></li>
<li>
@@ -92,22 +101,22 @@ components.</p>
</div>
<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 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>
+<span> name <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> speclist <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> unload <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<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="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">
@@ -123,76 +132,112 @@ 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
+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></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></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></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></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></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>,
+
+
+<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
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>
+
+
</dl><p>A list for use with <code>mkinmod</code>.</p>
</div>
<div id="details">
@@ -202,7 +247,7 @@ 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" class="external-link">pkgbuild::has_compiler()</a></code> and there
+<p>If a C compiler is found by <code><a href="https://r-lib.github.io/pkgbuild/reference/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" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p>
@@ -230,16 +275,16 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<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>
+ <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">&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>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><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>,</span></span>
+<span class="r-in"><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></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-in"><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">SFO_SFO</span><span class="op">)</span></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>
@@ -252,30 +297,32 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<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-in"><span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><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></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span>
+<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span>
+<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op">&lt;-</span> <span class="st">"~/.local/share/mkin"</span></span></span>
+<span class="r-in"><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" 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>
+<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><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>,</span></span>
+<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">#&gt;</span> Copied DLL from /tmp/RtmpelWAOB/fileb43c31a25a86.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>
+<span class="r-in"><span><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>
+<span class="r-in"><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" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span>
+<span class="r-in"><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></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><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>,</span></span>
+<span class="r-in"><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></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>
@@ -297,10 +344,10 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<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-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span>
+<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></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>
@@ -316,21 +363,21 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<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>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55555f013820&gt;</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>
+<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><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" 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>
+<span class="r-in"><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></span>
+<span class="r-in"><span> 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>
+<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><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></span>
+<span class="r-in"><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>,</span></span>
+<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
</code></pre></div>
</div>
</div>
@@ -345,7 +392,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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