Merge branch 'main' into custom_lsoda_call

1 files changed, 56 insertions, 33 deletions

diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html
index 27da5718..caeb25a1 100644
--- a/docs/reference/f_time_norm_focus.html
+++ b/docs/reference/f_time_norm_focus.html
@@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- 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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
       </span>
     </div>
 
@@ -45,19 +45,25 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax
       <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>
     <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>
@@ -89,56 +95,73 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="co"># S3 method for numeric</span>
-<span class="fu">f_time_norm_focus</span><span class="op">(</span>
-  <span class="va">object</span>,
-  moisture <span class="op">=</span> <span class="cn">NA</span>,
-  field_moisture <span class="op">=</span> <span class="cn">NA</span>,
-  temperature <span class="op">=</span> <span class="va">object</span>,
-  Q10 <span class="op">=</span> <span class="fl">2.58</span>,
-  walker <span class="op">=</span> <span class="fl">0.7</span>,
-  f_na <span class="op">=</span> <span class="cn">NA</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="co"># S3 method for mkindsg</span>
-<span class="fu">f_time_norm_focus</span><span class="op">(</span>
-  <span class="va">object</span>,
-  study_moisture_ref_source <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><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>,
-  Q10 <span class="op">=</span> <span class="fl">2.58</span>,
-  walker <span class="op">=</span> <span class="fl">0.7</span>,
-  f_na <span class="op">=</span> <span class="cn">NA</span>,
-  <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for numeric</span></span>
+<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  field_moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  temperature <span class="op">=</span> <span class="va">object</span>,</span>
+<span>  Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span>
+<span>  walker <span class="op">=</span> <span class="fl">0.7</span>,</span>
+<span>  f_na <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkindsg</span></span>
+<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  study_moisture_ref_source <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><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>,</span>
+<span>  Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span>
+<span>  walker <span class="op">=</span> <span class="fl">0.7</span>,</span>
+<span>  f_na <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>object</dt>
 <dd><p>An object containing information used for the calculations</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Currently not used</p></dd>
+
+
 <dt>moisture</dt>
 <dd><p>Numeric vector of moisture contents in \% w/w</p></dd>
+
+
 <dt>field_moisture</dt>
 <dd><p>Numeric vector of moisture contents at field capacity
 (pF2) in \% w/w</p></dd>
+
+
 <dt>temperature</dt>
 <dd><p>Numeric vector of temperatures in °C</p></dd>
+
+
 <dt>Q10</dt>
 <dd><p>The Q10 value used for temperature normalisation</p></dd>
+
+
 <dt>walker</dt>
 <dd><p>The Walker exponent used for moisture normalisation</p></dd>
+
+
 <dt>f_na</dt>
 <dd><p>The factor to use for NA values. If set to NA, only factors
 for complete cases will be returned.</p></dd>
+
+
 <dt>study_moisture_ref_source</dt>
 <dd><p>Source for the reference value
 used to calculate the study moisture. If 'auto', preference is given
 to a reference moisture given in the meta information, otherwise
 the focus soil moisture for the soil class is used</p></dd>
+
 </dl></div>
     <div id="references">
     <h2>References</h2>
@@ -160,10 +183,10 @@ Version 1.1, 18 December 2014
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.373956</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                                 study usda_soil_type study_moisture_ref_type</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Mississippi                Cohen 1991      Silt loam                    &lt;NA&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fayette     Liu and Adelfinskaya 2011      Silt loam                     pF1</span>
@@ -176,9 +199,9 @@ Version 1.1, 18 December 2014
 <span class="r-out co"><span class="r-pr">#&gt;</span> RefSol 03-G          0.5          20</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Site E1              0.5          20</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Site I2              0.5          20</span>
-<span class="r-in"><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span>
-<span class="r-in"><span class="co"># temperature only normalisation as in the EU evaluation</span></span>
-<span class="r-in"><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span></span>
+<span class="r-in"><span><span class="co"># temperature only normalisation as in the EU evaluation</span></span></span>
+<span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> $f_time_norm was (re)set to normalised values</span>
 </code></pre></div>
     </div>
@@ -194,7 +217,7 @@ Version 1.1, 18 December 2014
 </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>
 
       </footer></div>