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diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html index 646b534..5d7d5b3 100644 --- a/docs/articles/gmkin_manual.html +++ b/docs/articles/gmkin_manual.html @@ -1,18 +1,18 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><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=1.0"> <title>Manual for gmkin • gmkin</title> -<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<!-- 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 --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> <script src="../pkgdown.js"></script><meta property="og:title" content="Manual for gmkin"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- 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><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -22,14 +22,15 @@ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">gmkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span> </span> </div> @@ -75,7 +76,7 @@ <h1>Manual for gmkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-09-13</h4> + <h4 class="date">2019-03-14</h4> <div class="hidden name"><code>gmkin_manual.Rmd</code></div> @@ -94,11 +95,11 @@ <h2 class="hasAnchor"> <a href="#starting-gmkin" class="anchor"></a>Starting gmkin</h2> <p>As gmkin is an R package, you need to start R and load the gmkin package before you can run gmkin. The latter can be achieved by entering the command</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(gmkin)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(gmkin)</a></code></pre></div> <p>into the R console. This will also load the packages that gmkin depends on, most notably gWidgetsWWW2 and mkin. Loading the package only has to be done once after you have started R.</p> <p>Before you start gmkin, you should make sure that R is using the working directory that you would like to keep your gmkin project file(s) in. If you use the standard R GUI application on windows, you can change the working directory from the File menu (‘File’ -> ‘Change dir…’).</p> <p>Once you are sure that the working directory is what you want it to be, gmkin can be started by entering the R command</p> -<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="../reference/gmkin.html">gmkin</a></span>()</a></code></pre></div> +<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="../reference/gmkin.html">gmkin</a></span>()</a></code></pre></div> <p>This will cause the default browser to start up or, if it is already running, to pop up and open a new tab for displaying the gmkin user interface.</p> <p>In the R console, you should see a message that the httpd help server is started, if it wasn’t already started before.</p> <p>In the browser, you should see something like the screenshot below.</p> @@ -160,9 +161,9 @@ <a href="#importing-data-from-text-files" class="anchor"></a>Importing data from text files</h3> <p>In case you want to work with a larger dataset that is already available as a computer file e.g. in a spreadsheet application, you can export these data as a tab separated or comma separated text file and import it using the “Browse” and “Upload” buttons in the dataset editor.</p> <p>As an example, we can create a text file from one of the datasets shipped with the mkin package using the following R command:</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">write.table</span>(schaefer07_complex_case, <span class="dt">sep =</span> <span class="st">","</span>, <span class="dt">dec =</span> <span class="st">"."</span>, </a> -<a class="sourceLine" id="cb3-2" data-line-number="2"> <span class="dt">row.names =</span> <span class="ot">FALSE</span>, <span class="dt">quote =</span> <span class="ot">FALSE</span>, </a> -<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="dt">file =</span> <span class="st">"schaefer07.csv"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/write.table">write.table</a></span>(schaefer07_complex_case, <span class="dt">sep =</span> <span class="st">","</span>, <span class="dt">dec =</span> <span class="st">"."</span>,</a> +<a class="sourceLine" id="cb3-2" title="2"> <span class="dt">row.names =</span> <span class="ot">FALSE</span>, <span class="dt">quote =</span> <span class="ot">FALSE</span>,</a> +<a class="sourceLine" id="cb3-3" title="3"> <span class="dt">file =</span> <span class="st">"schaefer07.csv"</span>)</a></code></pre></div> <p>This produces a text file with comma separated values in the current working directory of R.</p> <p>Loading this text file into gmkin using the “Browse” and “Upload” buttons</p> <div class="figure"> @@ -241,23 +242,23 @@ <h3 class="hasAnchor"> <a href="#fitting-the-model" class="anchor"></a>Fitting the model</h3> <p>In many cases the starting parameters and the fit options do not need to be modified and the model fitting process can simply be started by pressing the “Run fit” button. In the R console, the progressive reduction in the model cost can be monitored and will be displayed in the following way:</p> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">Model cost at call <span class="dv">1</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span> </a> -<a class="sourceLine" id="cb4-2" data-line-number="2">Model cost at call <span class="dv">3</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span> </a> -<a class="sourceLine" id="cb4-3" data-line-number="3">Model cost at call <span class="dv">7</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> </a> -<a class="sourceLine" id="cb4-4" data-line-number="4">Model cost at call <span class="dv">8</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> </a> -<a class="sourceLine" id="cb4-5" data-line-number="5">Model cost at call <span class="dv">11</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> </a> -<a class="sourceLine" id="cb4-6" data-line-number="6">Model cost at call <span class="dv">12</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span> </a> -<a class="sourceLine" id="cb4-7" data-line-number="7">Model cost at call <span class="dv">15</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span> </a> -<a class="sourceLine" id="cb4-8" data-line-number="8">Model cost at call <span class="dv">17</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6367</span> </a> -<a class="sourceLine" id="cb4-9" data-line-number="9">Model cost at call <span class="dv">18</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6366</span> </a> -<a class="sourceLine" id="cb4-10" data-line-number="10">Model cost at call <span class="dv">22</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span> </a> -<a class="sourceLine" id="cb4-11" data-line-number="11">Model cost at call <span class="dv">23</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span> </a> -<a class="sourceLine" id="cb4-12" data-line-number="12">Model cost at call <span class="dv">27</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span> </a> -<a class="sourceLine" id="cb4-13" data-line-number="13">Model cost at call <span class="dv">28</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span> </a> -<a class="sourceLine" id="cb4-14" data-line-number="14">Model cost at call <span class="dv">32</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> </a> -<a class="sourceLine" id="cb4-15" data-line-number="15">Model cost at call <span class="dv">36</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> </a> -<a class="sourceLine" id="cb4-16" data-line-number="16">Model cost at call <span class="dv">37</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> </a> -<a class="sourceLine" id="cb4-17" data-line-number="17">Optimisation by method Port successfully terminated.</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">Model cost at call <span class="dv">1</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span></a> +<a class="sourceLine" id="cb4-2" title="2">Model cost at call <span class="dv">3</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span></a> +<a class="sourceLine" id="cb4-3" title="3">Model cost at call <span class="dv">7</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span></a> +<a class="sourceLine" id="cb4-4" title="4">Model cost at call <span class="dv">8</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span></a> +<a class="sourceLine" id="cb4-5" title="5">Model cost at call <span class="dv">11</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span></a> +<a class="sourceLine" id="cb4-6" title="6">Model cost at call <span class="dv">12</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span></a> +<a class="sourceLine" id="cb4-7" title="7">Model cost at call <span class="dv">15</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span></a> +<a class="sourceLine" id="cb4-8" title="8">Model cost at call <span class="dv">17</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6367</span></a> +<a class="sourceLine" id="cb4-9" title="9">Model cost at call <span class="dv">18</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6366</span></a> +<a class="sourceLine" id="cb4-10" title="10">Model cost at call <span class="dv">22</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span></a> +<a class="sourceLine" id="cb4-11" title="11">Model cost at call <span class="dv">23</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span></a> +<a class="sourceLine" id="cb4-12" title="12">Model cost at call <span class="dv">27</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span></a> +<a class="sourceLine" id="cb4-13" title="13">Model cost at call <span class="dv">28</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span></a> +<a class="sourceLine" id="cb4-14" title="14">Model cost at call <span class="dv">32</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span></a> +<a class="sourceLine" id="cb4-15" title="15">Model cost at call <span class="dv">36</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span></a> +<a class="sourceLine" id="cb4-16" title="16">Model cost at call <span class="dv">37</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span></a> +<a class="sourceLine" id="cb4-17" title="17">Optimisation by method Port successfully terminated.</a></code></pre></div> <p>If plotting of the fitting progress was selected, a new separate graphics window should either pop up, or a graphics window previously started for this purpose will be reused.</p> <p>If your screen size allows for it, you can arrange the R plotting window and the R console in a way that you can see everything at the same time:</p> <div class="figure"> @@ -281,7 +282,7 @@ <h3 class="hasAnchor"> <a href="#confidence-interval-plots" class="anchor"></a>Confidence interval plots</h3> <p>Whenever a new fit has been configured or a run of a fit has been completed, the plotting area is updated with the abovementioned plot of the data and the current model solution.</p> -<p>In addition, a confidence interval plot is shown below this conventional plot. In case a fit has been run and confidence intervals were successfully calculated for the fit (i.e. if the model was not overparameterised and no other problems occurred), the confidence intervals are graphically displayed as bars as shown below.</p> +<p>In addition, a confidence interval plot is shown below this conventional plot. In case a fit has been run and confidence intervals were successfully calculated for the fit ( i.e. if the model was not overparameterised and no other problems occurred), the confidence intervals are graphically displayed as bars as shown below.</p> <div class="figure"> <img src="img/confidence.png" alt="confidence"><p class="caption">confidence</p> </div> @@ -290,7 +291,7 @@ <div id="howtos" class="section level2"> <h2 class="hasAnchor"> <a href="#howtos" class="anchor"></a>Howtos</h2> -<p>The following sections show step by step descriptions of how to perform certain tasks using gmkin. In principle, this should be necessary as the GUI was designed to be largely self-explanatory. Nevertheless may help a beginner to understand how to use gmkin. At the same time, the gmkin author uses them as test cases to make sure that the most important functionality is not broken before releasing a new version.</p> +<p>The following sections show step by step descriptions of how to perform certain tasks using gmkin. In principle, this should not be necessary as the GUI was designed to be largely self-explanatory. Nevertheless it may help a beginner to understand how to use gmkin. At the same time, the gmkin author uses them as test cases to make sure that the most important functionality is not broken before releasing a new version.</p> <div id="use-a-model-and-a-dataset-from-a-built-in-workspace" class="section level3"> <h3 class="hasAnchor"> <a href="#use-a-model-and-a-dataset-from-a-built-in-workspace" class="anchor"></a>1. Use a model and a dataset from a built-in workspace</h3> @@ -399,9 +400,8 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> </div> - </footer> </div> |