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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/reference/f_time_norm_focus.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/reference/f_time_norm_focus.html')
-rw-r--r--docs/reference/f_time_norm_focus.html89
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>
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