diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-06-28 00:44:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-06-28 01:30:00 +0200 |
| commit | ef7ccf68e086bac3e75858bd4b97e3a2c6872aa1 (patch) | |
| tree | e1b9e55736b0961843e84c60caeb9117e1c35c6d /inst/web/add_err.html | |
| parent | 4672c2b3fd6c22e63b00ee5038998dd68a885c25 (diff) | |
Avoid multicore fits in vignettes for passing CRAN checks
Also a small fix to the FOCUS Z vignette, and an update
of the static documentation generated by staticdocs.
Diffstat (limited to 'inst/web/add_err.html')
| -rw-r--r-- | inst/web/add_err.html | 200 |
1 files changed, 200 insertions, 0 deletions
diff --git a/inst/web/add_err.html b/inst/web/add_err.html new file mode 100644 index 00000000..67ff8f70 --- /dev/null +++ b/inst/web/add_err.html @@ -0,0 +1,200 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>add_err. mkin 0.9.43</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" + Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="#">mkin 0.9.43</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> + </ul> + </div> + </div> + </div> +</div> + + <div class="container"> + <header> + + </header> + + <h1> + Add normally distributed errors to simulated kinetic degradation data +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><div>add_err(prediction, sdfunc, n = 1000, LOD = 0.1, reps = 2, digits = 1, seed = NA)</div></pre> + + <h2>Arguments</h2> + <dl> + <dt>prediction</dt> + <dd> + A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>. + </dd> + <dt>sdfunc</dt> + <dd> + 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. + </dd> + <dt>n</dt> + <dd> + The number of datasets to be generated. + </dd> + <dt>LOD</dt> + <dd> + The limit of detection (LOD). Values that are below the LOD after adding + the random error will be set to NA. + </dd> + <dt>reps</dt> + <dd> + The number of replicates to be generated within the datasets. + </dd> + <dt>digits</dt> + <dd> + The number of digits to which the values will be rounded. + </dd> + <dt>seed</dt> + <dd> + The seed used for the generation of random numbers. If NA, the seed + is not set. + </dd> + </dl> + + <div class="Description"> + <h2>Description</h2> + + <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="Value"> + <h2>Value</h2> + + <p><dl> + 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>. +</dl></p> + + </div> + + <div class="References"> + <h2>References</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 + http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'># The kinetic model +m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"), + M1 = mkinsub("SFO"), use_of_ff = "max") +</div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'> +# Generate a prediction for a specific set of parameters +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) + +# This is the prediction used for the "Type 2 datasets" on the Piacenza poster +# from 2015 +d_SFO_SFO <- mkinpredict(m_SFO_SFO, + c(k_parent = 0.1, f_parent_to_M1 = 0.5, + k_M1 = log(2)/1000), + c(parent = 100, M1 = 0), + sampling_times) + +# Add an error term with a constant (independent of the value) standard deviation +# of 10, and generate three datasets +d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 ) + +# Name the datasets for nicer plotting +names(d_SFO_SFO_err) <- paste("Dataset", 1:3) + +# Name the model in the list of models (with only one member in this case) +# for nicer plotting later on. +# Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets +# are easy and examples are run often. Use only one core not to offend CRAN +# checks +f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO), + d_SFO_SFO_err, cores = 1, + quiet = TRUE, method.modFit = "Marq") + +plot(f_SFO_SFO) +</div> +<p><img src='add_err-4.png' alt='' width='540' height='400' /></p> +<div class='input'> +# We would like to inspect the fit for dataset 3 more closely +# Using double brackets makes the returned object an mkinfit object +# instead of a list of mkinfit objects, so plot.mkinfit is used +plot(f_SFO_SFO[[3]], show_residuals = TRUE) +</div> +<p><img src='add_err-6.png' alt='' width='540' height='400' /></p> +<div class='input'> +# If we use single brackets, we should give two indices (model and dataset), +# and plot.mmkin is used +plot(f_SFO_SFO[1, 3]) +</div> +<p><img src='add_err-8.png' alt='' width='540' height='400' /></p> +<div class='input'></div></pre> + </div> + <div class="span4"> + <!-- <ul> + <li>add_err</li> + </ul> + <ul> + <li> manip </li> + </ul> --> + + + <h2>Author</h2> + + Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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