From 9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 20 Apr 2023 19:53:28 +0200
Subject: Fix and rebuild documentation, see NEWS

I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.

Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.
---
 docs/reference/mkinpredict.html | 84 ++++++++++++++++++++++++-----------------
 1 file changed, 49 insertions(+), 35 deletions(-)

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

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 2aab0b50..20ace74a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -19,13 +19,13 @@ kinetic parameters and initial values for the state variables."><!-- mathjax -->
       </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">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -36,6 +36,8 @@ kinetic parameters and initial values for the state variables."><!-- mathjax -->
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -43,22 +45,29 @@ kinetic parameters and initial values for the state variables."><!-- mathjax -->
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    <li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a>
@@ -66,6 +75,14 @@ kinetic parameters and initial values for the state variables."><!-- mathjax -->
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Miscellaneous</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>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
@@ -107,10 +124,11 @@ kinetic parameters and initial values for the state variables.</p>
 <span>  outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span>
 <span>  solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span>
 <span>  use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  use_symbols <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span>
 <span>  atol <span class="op">=</span> <span class="fl">1e-08</span>,</span>
 <span>  rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span>
-<span>  maxsteps <span class="op">=</span> <span class="fl">20000</span>,</span>
+<span>  maxsteps <span class="op">=</span> <span class="fl">20000L</span>,</span>
 <span>  map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  na_stop <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">...</span></span>
@@ -166,8 +184,9 @@ solver is used.</p></dd>
 <dd><p>The method that should be used for producing the
 predictions. This should generally be "analytical" if there is only one
 observed variable, and usually "deSolve" in the case of several observed
-variables. The third possibility "eigen" is faster but not applicable to
-some models e.g.  using FOMC for the parent compound.</p></dd>
+variables. The third possibility "eigen" is fast in comparison to uncompiled
+ODE models, but not applicable to some models, e.g. using FOMC for the
+parent compound.</p></dd>
 
 
 <dt>use_compiled</dt>
@@ -175,24 +194,27 @@ some models e.g.  using FOMC for the parent compound.</p></dd>
 <a href="mkinmod.html">mkinmod</a> model is used, even if is present.</p></dd>
 
 
+<dt>use_symbols</dt>
+<dd><p>If set to <code>TRUE</code> (default), symbol info present in
+the <a href="mkinmod.html">mkinmod</a> object is used if available for accessing compiled code</p></dd>
+
+
 <dt>method.ode</dt>
 <dd><p>The solution method passed via mkinpredict to ode] in
-case the solution type is "deSolve". The default "lsoda" is performant, but
-sometimes fails to converge.</p></dd>
+case the solution type is "deSolve" and we are not using compiled code.
+When using compiled code, only lsoda is supported.</p></dd>
 
 
 <dt>atol</dt>
-<dd><p>Absolute error tolerance, passed to ode. Default is 1e-8,
-lower than in lsoda.</p></dd>
+<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd>
 
 
 <dt>rtol</dt>
-<dd><p>Absolute error tolerance, passed to ode. Default is 1e-10,
-much lower than in lsoda.</p></dd>
+<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd>
 
 
 <dt>maxsteps</dt>
-<dd><p>Maximum number of steps, passed to ode.</p></dd>
+<dd><p>Maximum number of steps, passed to the ode solver.</p></dd>
 
 
 <dt>map_output</dt>
@@ -325,15 +347,15 @@ as these always return mapped output.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       time degradinol </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000  0.2478752 </span>
 <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
-<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"lsoda"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       time degradinol </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000  0.2478752 </span>
 <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
-<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"ode45"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       time degradinol </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000  0.2478752 </span>
 <span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
-<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-in"><span>      method <span class="op">=</span> <span class="st">"rk4"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       time degradinol </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000  0.2480043 </span>
 <span class="r-in"><span><span class="co"># rk4 is not as precise here</span></span></span>
@@ -373,25 +395,17 @@ as these always return mapped output.</p></dd>
 <span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled      1.0   0.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical      1.0   0.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen      5.5   0.022</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     51.0   0.204</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled        1   0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical        1   0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen        4   0.008</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve       30   0.060</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="co"># Predict from a fitted model</span></span></span>
 <span class="r-in"><span>  <span class="va">f</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_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">f</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_C</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-in"><span>  <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> DLSODA-  At current T (=R1), MXSTEP (=I1) steps   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       taken on this call before reaching TOUT     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, I1 = 1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 9.99904e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>an excessive amount of work (&gt; maxsteps ) was done, but integration was not successful - increase maxsteps</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Returning early. Results are accurate, as far as they go</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in out[available, var]:</span> (subscript) logical subscript too long</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in !is.null(x$symbols) &amp; use_symbols:</span> operations are possible only for numeric, logical or complex types</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
@@ -408,7 +422,7 @@ as these always return mapped output.</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
-- 
cgit v1.2.1