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-rw-r--r--R/set_nd_nq.R4
-rw-r--r--docs/404.html5
-rw-r--r--docs/authors.html5
-rw-r--r--docs/index.html2
-rw-r--r--docs/reference/index.html12
-rw-r--r--docs/reference/set_nd_nq.html44
-rw-r--r--man/set_nd_nq.Rd8
7 files changed, 27 insertions, 53 deletions
diff --git a/R/set_nd_nq.R b/R/set_nd_nq.R
index a372879..37b9a89 100644
--- a/R/set_nd_nq.R
+++ b/R/set_nd_nq.R
@@ -1,11 +1,11 @@
#' Set non-detects and unquantified values in residue series without replicates
-
+#'
#' This function automates replacing unquantified values in residue time and
#' depth series. For time series, the function performs part of the residue
#' processing proposed in the FOCUS kinetics guidance for parent compounds
#' and metabolites. For two-dimensional residue series over time and depth,
#' it automates the proposal of Boesten et al (2015).
-
+#'
#' @param res_raw Character vector of a residue time series, or matrix of
#' residue values with rows representing depth profiles for a specific sampling
#' time, and columns representing time series of residues at the same depth.
diff --git a/docs/404.html b/docs/404.html
index 8e5e550..f42956b 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -8,11 +8,13 @@
<title>Page not found (404) • pfm</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,10 +34,12 @@
+
<meta property="og:title" content="Page not found (404)" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -79,7 +83,6 @@
<a href="reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
diff --git a/docs/authors.html b/docs/authors.html
index ea71b72..05bd9d3 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -8,11 +8,13 @@
<title>Authors • pfm</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,10 +34,12 @@
+
<meta property="og:title" content="Authors" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -79,7 +83,6 @@
<a href="reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
diff --git a/docs/index.html b/docs/index.html
index 33b8434..23000f1 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -75,7 +75,7 @@
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"pfm"</span>)</a></code></pre></div>
<p>Alternatively you can install the package using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(devtools)</a>
-<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
</div>
<div id="use" class="section level2">
<h2 class="hasAnchor">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e9c7098..0608dd9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -8,11 +8,13 @@
<title>Function reference • pfm</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,10 +34,12 @@
+
<meta property="og:title" content="Function reference" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -79,7 +83,6 @@
<a href="../reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -172,12 +175,7 @@
<td>
<p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p>
</td>
- <td><p>Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).</p></td>
+ <td><p>Set non-detects and unquantified values in residue series without replicates</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html
index ff751dd..9ec17ea 100644
--- a/docs/reference/set_nd_nq.html
+++ b/docs/reference/set_nd_nq.html
@@ -6,18 +6,15 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015). — set_nd_nq • pfm</title>
+<title>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • pfm</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -37,15 +34,9 @@ it automates the proposal of Boesten et al (2015). — set_nd_nq • pfm</title>
-<meta property="og:title" content="Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015). — set_nd_nq" />
-<meta property="og:description" content="Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
+<meta property="og:title" content="Set non-detects and unquantified values in residue series without replicates — set_nd_nq" />
+<meta property="og:description" content="This function automates replacing unquantified values in residue time and
depth series. For time series, the function performs part of the residue
processing proposed in the FOCUS kinetics guidance for parent compounds
and metabolites. For two-dimensional residue series over time and depth,
@@ -54,6 +45,7 @@ it automates the proposal of Boesten et al (2015)." />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -97,7 +89,6 @@ it automates the proposal of Boesten et al (2015)." />
<a href="../reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -113,32 +104,24 @@ it automates the proposal of Boesten et al (2015)." />
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).</h1>
+ <h1>Set non-detects and unquantified values in residue series without replicates</h1>
<div class="hidden name"><code>set_nd_nq.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
+ <p>This function automates replacing unquantified values in residue time and
depth series. For time series, the function performs part of the residue
processing proposed in the FOCUS kinetics guidance for parent compounds
and metabolites. For two-dimensional residue series over time and depth,
it automates the proposal of Boesten et al (2015).</p>
-
</div>
<pre class="usage"><span class='fu'>set_nd_nq</span>(<span class='no'>res_raw</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_presence</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>set_nd_nq_focus</span>(<span class='no'>res_raw</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>set_first_sample_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>first_sample_nd_value</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>ignore_below_loq_after_first_nd</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>
@@ -182,18 +165,16 @@ in case it is a non-detection?</p></td>
non-detection that occurs after the quantified values?</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p>
-
<h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
<ul>
<li><p><code>set_nd_nq_focus</code>: Set non-detects in residue time series according to FOCUS rules</p></li>
</ul>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
@@ -204,7 +185,6 @@ Wageningen UR (University &amp; Research centre)</p>
<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
18 December 2014, p. 251</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># FOCUS (2014) p. 75/76 and 131/132</span>
@@ -249,13 +229,9 @@ Wageningen UR (University &amp; Research centre)</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#functions">Functions</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
index b2da429..47b7e33 100644
--- a/man/set_nd_nq.Rd
+++ b/man/set_nd_nq.Rd
@@ -3,12 +3,7 @@
\name{set_nd_nq}
\alias{set_nd_nq}
\alias{set_nd_nq_focus}
-\title{Set non-detects and unquantified values in residue series without replicates
-This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).}
+\title{Set non-detects and unquantified values in residue series without replicates}
\usage{
set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
@@ -45,7 +40,6 @@ non-detection that occurs after the quantified values?}
A numeric vector, if a vector was supplied, or a numeric matrix otherwise
}
\description{
-Set non-detects and unquantified values in residue series without replicates
This function automates replacing unquantified values in residue time and
depth series. For time series, the function performs part of the residue
processing proposed in the FOCUS kinetics guidance for parent compounds

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