From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 17 Nov 2022 14:54:20 +0100
Subject: Complete update of online docs for v1.2.0

---
 docs/reference/mkinmod.html | 188 +++++++++++++++++++++++++++-----------------
 1 file changed, 115 insertions(+), 73 deletions(-)

(limited to 'docs/reference/mkinmod.html')

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 3a29b39b..7dfa740a 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -21,7 +21,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
       </span>
     </div>
 
@@ -48,11 +48,14 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
       <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <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>
@@ -60,7 +63,10 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
       <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>
@@ -95,22 +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">
@@ -130,72 +136,108 @@ If the argument <code>use_of_ff</code> is set to "min"
 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">
@@ -233,16 +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>
@@ -255,32 +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></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 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/RtmpkcKjUM/file8dd657f864c2.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></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/Rtmp6DB2Bl/file3f5b93b53e71f.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 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"># 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>
@@ -302,10 +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>
@@ -321,21 +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: 0x55cc1a5f8ad8&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: 0x55556401ac50&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>
@@ -350,7 +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> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
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