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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-10 08:53:30 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-10 08:53:30 +0200
commita5e458ecb33ae87e46b2237174a194f6252a97cf (patch)
tree07f96162166021f73d823b61e96e5438e7dfb6d8 /docs
parent63df3871a442de4bf47e4d9de1449e7f6ed65b2f (diff)
Finish documentation of set_nd and test it
Diffstat (limited to 'docs')
-rw-r--r--docs/reference/index.html15
-rw-r--r--docs/reference/set_nd.html247
-rw-r--r--docs/sitemap.xml3
3 files changed, 265 insertions, 0 deletions
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e1acfc1..a704ad0 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -167,6 +167,21 @@
<p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p>
</td>
<td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="set_nd.html">set_nd()</a></code> <code><a href="set_nd.html">set_nd_focus()</a></code> </p>
+ </td>
+ <td><p>Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq.</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html
new file mode 100644
index 0000000..32ac155
--- /dev/null
+++ b/docs/reference/set_nd.html
@@ -0,0 +1,247 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+
+<title>Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq. — set_nd • pfm</title>
+
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+<meta property="og:title" content="Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq. — set_nd" />
+
+<meta property="og:description" content="Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq." />
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+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq.</h1>
+
+ <div class="hidden name"><code>set_nd.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Set non-detects in residue series without replicates
+Sets non-detects directly before or directly after detects to NA. Values between
+lod and loq are set to their mean value if an loq is specified.
+If 'time_zero' is set to TRUE, the residue series is assumed to start with time
+zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
+set_nd_focus variant, this is zero, otherwise this argument has NA as default
+value.
+If stopping after the first non-detection is requested, as in in the FOCUS
+variant of the function, an loq has to be specified in order to decide
+if any later detections are above the loq.</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>set_nd</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>time_zero_nd_value</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>stop_after_first_nondetect</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>set_nd_focus</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>r</th>
+ <td><p>A character vector of sequential residues without replicates, with
+non-detects specified as 'nd' and unquantified values above the limit of
+detection specified as 'nq', otherwise coercible to numeric</p></td>
+ </tr>
+ <tr>
+ <th>lod</th>
+ <td><p>Limit of detection (numeric)</p></td>
+ </tr>
+ <tr>
+ <th>loq</th>
+ <td><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to
+stop after the first non-detection is to be applied</p></td>
+ </tr>
+ <tr>
+ <th>time_zero</th>
+ <td><p>Is the first value in the series a time zero value?</p></td>
+ </tr>
+ <tr>
+ <th>time_zero_nd_value</th>
+ <td><p>Which value should we use for non-detects at time zero?</p></td>
+ </tr>
+ <tr>
+ <th>stop_after_first_nondetect</th>
+ <td><p>Should we really stop after the first non-detection?</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
+
+
+<ul>
+<li><p><code>set_nd_focus</code>: Set non-detects in residues series according to FOCUS rules</p></li>
+</ul>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2014) p. 75, 76, 131, 132</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>parent_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt; [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.06</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt; [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='no'>metabolite</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>0.03</span>, <span class='fl'>0.06</span>, <span class='fl'>0.10</span>, <span class='fl'>0.11</span>, <span class='fl'>0.10</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</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="#functions">Functions</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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+
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diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 6eff936..79d9b14 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -100,6 +100,9 @@
<loc>https://pkgdown.jrwb.de/pfm/reference/sawtooth.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/pfm/reference/set_nd.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html</loc>
</url>
<url>

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