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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-16 18:02:18 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-16 18:02:18 +0200
commitd81550d0cccae824cc748de48e7fd50ea8d8033a (patch)
treecb95252ff725b5dcd0237bb8f74fdac4a3e08d15 /docs/reference/TOXSWA_cwa.html
parent4bc95b3e4aae22e4052e0a4c905a9227c909e2cd (diff)
Make na.rm = FALSE the default for geomean()
This makes more sense and is in line with mean() from base R. Adapt tests and update docs.
Diffstat (limited to 'docs/reference/TOXSWA_cwa.html')
-rw-r--r--docs/reference/TOXSWA_cwa.html97
1 files changed, 72 insertions, 25 deletions
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 8939850..cedb023 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -8,11 +8,13 @@
<title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title>
+
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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@@ -32,14 +34,15 @@
-<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
+<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -83,7 +86,6 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<a href="../reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -105,23 +107,33 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
</div>
<div class="ref-description">
-
<p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
-
</div>
- <pre class="usage"><span class='no'>TOXSWA_cwa</span></pre>
-
+
+
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An <code>R6Class</code> generator object.</p>
-
- <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+ <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
<dl class='dl-horizontal'>
+ <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value
+ in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
+ adsorbed to suspended matter will be used. The resulting dataframe is stored in the
+ <code>events</code> field of the object.</p></dd>
+ <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above.
+ Again, if <code>total = TRUE</code>, the total concentration including the amount
+ adsorbed to suspended matter will be used.</p></dd>
+
+</dl>
+
+ <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+
+ <p><div class="r6-fields"></p><dl class='dl-horizontal'>
<dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd>
<dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd>
@@ -136,24 +148,62 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
for the requested moving window sizes in days.</p></dd>
-</dl>
-
+</dl><p></div></p>
<h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+<h3>Public methods</h3>
-<dl class='dl-horizontal'>
- <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value
- in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
- adsorbed to suspended matter will be used. The resulting dataframe is stored in the
- <code>events</code> field of the object.</p></dd>
- <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above.
- Again, if <code>total = TRUE</code>, the total concentration including the amount
- adsorbed to suspended matter will be used.</p></dd>
+<ul>
+<li><p><a href='#method-new'><code>TOXSWA_cwa$new()</code></a></p></li>
+<li><p><a href='#method-moving_windows'><code>TOXSWA_cwa$moving_windows()</code></a></p></li>
+<li><p><a href='#method-get_events'><code>TOXSWA_cwa$get_events()</code></a></p></li>
+<li><p><a href='#method-print'><code>TOXSWA_cwa$print()</code></a></p></li>
+<li><p><a href='#method-clone'><code>TOXSWA_cwa$clone()</code></a></p></li>
+</ul>
+<p><hr>
+<a id="method-new"></a></p><h3>Method <code>new()</code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$new(
+ filename,
+ basedir,
+ zipfile = NULL,
+ segment = "last",
+ substance = "parent",
+ total = FALSE
+)</pre><p></div></p>
+
+<p><hr>
+<a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$moving_windows(windows, total = FALSE)</pre><p></div></p>
+
+<p><hr>
+<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$get_events(thresholds, total = FALSE)</pre><p></div></p>
+
+<p><hr>
+<a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$print()</pre><p></div></p>
+
+<p><hr>
+<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3>
+<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$clone(deep = FALSE)</pre><p></div></p>
+
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl class='dl-horizontal'>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
+
+</dl><p></div></p>
-</dl>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
@@ -192,13 +242,10 @@ for the requested moving window sizes in days.</p></dd>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#format">Format</a></li>
-
- <li><a href="#fields">Fields</a></li>
-
<li><a href="#methods">Methods</a></li>
-
+ <li><a href="#public-fields">Public fields</a></li>
+ <li><a href="#methods">Methods</a></li>
<li><a href="#examples">Examples</a></li>
</ul>

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