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authorJohannes Ranke <jranke@uni-bremen.de>2017-01-19 10:36:19 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-19 10:36:19 +0100
commitdd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 (patch)
treea954197c4e8e093d4b08c08eab14753b58602ff4 /docs/reference
parent3ead7acba845b4f2552f555dfb29da889ed0cda8 (diff)
Move mkin::twa to pfm::max_twa.mkinfit
- Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but never released with it - Add a test to check max_twa.one_box() against analytical solutions in max_twa.mkinfit(). - Clean up R CMD check - Update docs
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/max_twa.html45
-rw-r--r--docs/reference/one_box-4.pngbin5743 -> 5587 bytes
-rw-r--r--docs/reference/one_box-8.pngbin9901 -> 9860 bytes
-rw-r--r--docs/reference/one_box.html12
-rw-r--r--docs/reference/plot.one_box-8.pngbin13603 -> 13490 bytes
-rw-r--r--docs/reference/sawtooth-6.pngbin13603 -> 13490 bytes
-rw-r--r--docs/reference/sawtooth.html4
7 files changed, 53 insertions, 8 deletions
diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index 4bb1be9..f78da58 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -70,7 +70,11 @@
</div>
- <p>The maximum time weighted average concentration for a moving window</p>
+ <p>If you generate your time series using <code><a href='sawtooth.html'>sawtooth</a></code>,
+you need to make sure that the length of the time series allows
+for finding the maximum. It is therefore recommended to check this using
+<code><a href='plot.one_box.html'>plot.one_box</a></code> using the window size for the argument
+<code>max_twa</code>.</p>
<pre><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre>
@@ -83,19 +87,56 @@
<dd>The size of the moving window</dd>
</dl>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The method working directly on fitted <code>mkinfit</code> objects uses the
+equations given in the PEC soil section of the FOCUS guidance and is restricted
+SFO, FOMC and DFOP models and to the parent compound</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<p><code><a href='twa.html'>twa</a></code></p>
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>),
+ <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
+<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#&gt; $max
+#&gt; parent
+#&gt; 0.9537545
+#&gt;
+#&gt; $window_start
+#&gt; parent
+#&gt; 0
+#&gt;
+#&gt; $window_end
+#&gt; parent
+#&gt; 21
+#&gt; </div><div class='input'><span class='no'>pred_FOMC</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>max_twa</span>(<span class='no'>pred_FOMC</span>)</div><div class='output co'>#&gt; 21
+#&gt; 18.22124 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
+ <li><a href="#details">Details</a></li>
+
+ <li><a href="#references">References</a></li>
+
<li><a href="#see-also">See also</a></li>
- </ul>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
</div>
</div>
diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png
index 10ebb35..3c6dadb 100644
--- a/docs/reference/one_box-4.png
+++ b/docs/reference/one_box-4.png
Binary files differ
diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png
index 31e2f4b..897737e 100644
--- a/docs/reference/one_box-8.png
+++ b/docs/reference/one_box-8.png
Binary files differ
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 698f887..cb49c02 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -74,22 +74,26 @@
This does not create objects of type <code>ts</code>.</p>
- <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+ <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
<span class='co'># S3 method for numeric</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
<span class='co'># S3 method for character</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+ <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"model"</span>, <span class='fl'>1</span>), <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+ <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
<dl class="dl-horizontal">
<dt>x</dt>
<dd>When numeric, this is the half-life to be used for an exponential
decline. If x is an mkinfit object, the decline is calculated from this object</dd>
+ <dt>ini</dt>
+ <dd>The initial amount for each compound</dd>
<dt>...</dt>
<dd>Further arguments passed to methods</dd>
<dt>t_end</dt>
diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png
index 161ecb4..f534444 100644
--- a/docs/reference/plot.one_box-8.png
+++ b/docs/reference/plot.one_box-8.png
Binary files differ
diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png
index 161ecb4..f534444 100644
--- a/docs/reference/sawtooth-6.png
+++ b/docs/reference/sawtooth-6.png
Binary files differ
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index cf33630..216f64a 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -102,8 +102,8 @@ the corresponding amounts applied in the second column.</dd>
<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='sawtooth-6.png' alt='' width='540' height='400' /><div class='input'>
<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
-#&gt; parent m1
-#&gt; 0.6627707 0.8542785
+#&gt; parent m1
+#&gt; 66.01096 85.08484
#&gt;
#&gt; $window_start
#&gt; parent m1

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