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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:16:17 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:27:50 +0100
commitaed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 (patch)
tree7ca136834857c12449f50a1e086a589cc9b79e2e /docs/reference/pfm_degradation.html
parent64f629efbe666bae56f48a309adf33d1eb09c358 (diff)
Reorganise data generation
- Use inst/data_generation for R code generating data as in some of my other packages - data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff contents were not changed - Remove ChangeLog, the history is in the git logs - Update docs and some links contained therein - use \doi{} markup - Move logs to log directory
Diffstat (limited to 'docs/reference/pfm_degradation.html')
-rw-r--r--docs/reference/pfm_degradation.html210
1 files changed, 72 insertions, 138 deletions
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index 8d06107..724a1aa 100644
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<a class="navbar-link" href="../index.html">pfm</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span>
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<h1>Calculate a time course of relative concentrations based on an mkinmod model</h1>
@@ -112,80 +43,83 @@
<p>Calculate a time course of relative concentrations based on an mkinmod model</p>
</div>
- <pre class="usage"><span class='fu'>pfm_degradation</span>(
- <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>,
- <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
- <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>),
- <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>)
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>model</th>
- <td><p>The degradation model to be used. Either a parent only model like
-'SFO' or 'FOMC', or an mkinmod object</p></td>
- </tr>
- <tr>
- <th>DT50</th>
- <td><p>The half-life. This is only used when simple exponential decline
-is calculated (SFO model).</p></td>
- </tr>
- <tr>
- <th>parms</th>
- <td><p>The parameters used for the degradation model</p></td>
- </tr>
- <tr>
- <th>years</th>
- <td><p>For how many years should the degradation be predicted?</p></td>
- </tr>
- <tr>
- <th>step_days</th>
- <td><p>What step size in days should the output have?</p></td>
- </tr>
- <tr>
- <th>times</th>
- <td><p>The output times</p></td>
- </tr>
- </table>
-
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt; time parent
-#&gt; 0 0 1.0000000
-#&gt; 1 1 0.9330330
-#&gt; 2 2 0.8705506
-#&gt; 3 3 0.8122524
-#&gt; 4 4 0.7578583
-#&gt; 5 5 0.7071068</div></pre>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pfm_degradation</span><span class="op">(</span></span>
+<span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span>
+<span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span> parms <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>k_parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="va">DT50</span><span class="op">)</span>,</span>
+<span> years <span class="op">=</span> <span class="fl">1</span>,</span>
+<span> step_days <span class="op">=</span> <span class="fl">1</span>,</span>
+<span> times <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="va">years</span> <span class="op">*</span> <span class="fl">365</span>, by <span class="op">=</span> <span class="va">step_days</span><span class="op">)</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>model</dt>
+<dd><p>The degradation model to be used. Either a parent only model like
+'SFO' or 'FOMC', or an mkinmod object</p></dd>
+
+
+<dt>DT50</dt>
+<dd><p>The half-life. This is only used when simple exponential decline
+is calculated (SFO model).</p></dd>
+
+
+<dt>parms</dt>
+<dd><p>The parameters used for the degradation model</p></dd>
+
+
+<dt>years</dt>
+<dd><p>For how many years should the degradation be predicted?</p></dd>
+
+
+<dt>step_days</dt>
+<dd><p>What step size in days should the output have?</p></dd>
+
+
+<dt>times</dt>
+<dd><p>The output times</p></dd>
+
+</dl></div>
+ <div id="author">
+ <h2>Author</h2>
+ <p>Johannes Ranke</p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><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">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time parent</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 1.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 0.9330330</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 0.8705506</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 3 0.8122524</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 4 0.7578583</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 5 0.7071068</span>
+</code></pre></div>
+ </div>
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