1 files changed, 216 insertions, 0 deletions
diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html
new file mode 100644
index 00000000..00a2b1d0
--- /dev/null
+++ b/docs/dev/reference/add_err.html
@@ -0,0 +1,216 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err"><meta name="description" content="Normally distributed errors are added to data predicted for a specific
+degradation model using mkinpredict. The variance of the error
+may depend on the predicted value and is specified as a standard deviation."><meta property="og:description" content="Normally distributed errors are added to data predicted for a specific
+degradation model using mkinpredict. The variance of the error
+may depend on the predicted value and is specified as a standard deviation."><meta name="robots" content="noindex"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">mkin</a>
+
+    <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li>
+    <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
+    <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li>
+    <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li>
+    <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Add normally distributed errors to simulated kinetic degradation data</h1>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small>
+      <div class="d-none name"><code>add_err.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Normally distributed errors are added to data predicted for a specific
+degradation model using <code><a href="mkinpredict.html">mkinpredict</a></code>. The variance of the error
+may depend on the predicted value and is specified as a standard deviation.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span>
+<span>  <span class="va">prediction</span>,</span>
+<span>  <span class="va">sdfunc</span>,</span>
+<span>  secondary <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><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">10</span>,</span>
+<span>  LOD <span class="op">=</span> <span class="fl">0.1</span>,</span>
+<span>  reps <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  digits <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  seed <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-prediction">prediction<a class="anchor" aria-label="anchor" href="#arg-prediction"></a></dt>
+<dd><p>A prediction from a kinetic model as produced by
+<code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd>
+
+
+<dt id="arg-sdfunc">sdfunc<a class="anchor" aria-label="anchor" href="#arg-sdfunc"></a></dt>
+<dd><p>A function taking the predicted value as its only argument and
+returning a standard deviation that should be used for generating the
+random error terms for this value.</p></dd>
+
+
+<dt id="arg-secondary">secondary<a class="anchor" aria-label="anchor" href="#arg-secondary"></a></dt>
+<dd><p>The names of state variables that should have an initial
+value of zero</p></dd>
+
+
+<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
+<dd><p>The number of datasets to be generated.</p></dd>
+
+
+<dt id="arg-lod">LOD<a class="anchor" aria-label="anchor" href="#arg-lod"></a></dt>
+<dd><p>The limit of detection (LOD). Values that are below the LOD after
+adding the random error will be set to NA.</p></dd>
+
+
+<dt id="arg-reps">reps<a class="anchor" aria-label="anchor" href="#arg-reps"></a></dt>
+<dd><p>The number of replicates to be generated within the datasets.</p></dd>
+
+
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
+<dd><p>The number of digits to which the values will be rounded.</p></dd>
+
+
+<dt id="arg-seed">seed<a class="anchor" aria-label="anchor" href="#arg-seed"></a></dt>
+<dd><p>The seed used for the generation of random numbers. If NA, the
+seed is not set.</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the
+components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is
+the question. XV Symposium on Pesticide Chemistry 2-4 September 2015,
+Piacenza, Italy
+https://jrwb.de/posters/piacenza_2015.pdf</p>
+    </div>
+    <div class="section level2">
+    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+    <p>Johannes Ranke</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The kinetic model</span></span></span>
+<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                     M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span>
+<span class="r-in"><span><span class="va">sampling_times</span> <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><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span>
+<span class="r-in"><span><span class="co"># from 2015</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span>
+<span class="r-in"><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="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
+<span class="r-in"><span>                           k_M1 <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="fl">1000</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                         <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                         <span class="va">sampling_times</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span>
+<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span>
+<span class="r-in"><span><span class="co"># nicer plotting later on.  Be quiet and use only one core not to offend CRAN</span></span></span>
+<span class="r-in"><span><span class="co"># checks</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                   <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span>
+<span class="r-in"><span>                   quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span>
+<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span>
+<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span>
+<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+