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diff --git a/docs/index.html b/docs/index.html index 0df4c29..a9c7511 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,20 +1,20 @@ <!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>Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data • 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="Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data"> <meta property="og:description" content="Browser based graphical user interface for R package mkin, based on the gWidgetsWWW2 package. Both gmkin and gWidgetsWWW2 are developed on GitHub, but are also available from the R-Forge repository."> <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]--> @@ -24,14 +24,15 @@ <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> @@ -73,7 +74,7 @@ </header><div class="row"> <div class="contents col-md-9"> - <div id="gmkin" class="section level1"> +<div id="gmkin" class="section level1"> <div class="page-header"><h1 class="hasAnchor"> <a href="#gmkin" class="anchor"></a>gmkin</h1></div> <p>The R package <a href="https://pkgdown.jrwb.de/gmkin">gmkin</a> provides a browser based graphical user interface (GUI) for fitting kinetic models to chemical degradation data based on R package <a href="https://pkgdown.jrwb.de/mkin">mkin</a>. The GUI is based on the <a href="http://github.com/jverzani/gWidgetsWWW2">gWidgetsWWW2</a> package developed by John Verzani. The GUI elements are created by the JavaScript library ExtJS which is bundled with gWidgetsWWW2.</p> @@ -93,15 +94,15 @@ <h3 class="hasAnchor"> <a href="#installing-gmkin-and-gwidgetswww2" class="anchor"></a>Installing gmkin and gWidgetsWWW2</h3> <p>Windows and Linux users running R 3.1.0 or later can make use of my drat package repository on github. Before installing gmkin, you should update your R packages already installed, e.g. by starting R, and pasting the command</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb1-1" data-line-number="1">update.packages()</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb1-1" title="1">update.packages()</a></code></pre></div> <p>or similar, depending on your R installation.</p> <p>For installing gmkin or upgrading to the latest released version, please install the drat package</p> -<div class="sourceCode" id="cb2"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb2-1" data-line-number="1">install.packages(<span class="st">"drat"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb2-1" title="1">install.packages(<span class="st">"drat"</span>)</a></code></pre></div> <p>add my repository</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb3"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb3-1" title="1"><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</a></code></pre></div> <p>and install as usual</p> -<div class="sourceCode" id="cb4"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb4-1" data-line-number="1">install.packages(<span class="st">"gmkin"</span>)</a></code></pre></div> -<p>The latest changes to gmkin are recorded in the <a href="https://github.com/jranke/gmkin/blob/master/NEWS.html">NEWS</a> file, more details can be found in the <a href="https://github.com/jranke/gmkin/commits/master">commit history</a>.</p> +<div class="sourceCode" id="cb4"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb4-1" title="1">install.packages(<span class="st">"gmkin"</span>)</a></code></pre></div> +<p>The latest changes to gmkin are recorded in the <a href="https://github.com/jranke/gmkin/blob/master/NEWS.md">NEWS</a> file, more details can be found in the <a href="https://github.com/jranke/gmkin/commits/master">commit history</a>.</p> <p><img src="gmkin_screenshot.png" alt="gmkin screenshot"></p> </div> </div> @@ -109,9 +110,9 @@ <h2 class="hasAnchor"> <a href="#usage" class="anchor"></a>Usage</h2> <p>Without further preparation, you can start the GUI by starting R and pasting the following commands into the R terminal (R console on Windows):</p> -<div class="sourceCode" id="cb5"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb5-1" data-line-number="1">require(gmkin)</a> -<a class="sourceLine" id="cb5-2" data-line-number="2">gmkin()</a></code></pre></div> -<p>You may also want to adapt the browser that R starts (using e.g. <code>options(browser="/usr/bin/firefox")</code> on linux, or setting the default browser on Windows).</p> +<div class="sourceCode" id="cb5"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb5-1" title="1">require(gmkin)</a> +<a class="sourceLine" id="cb5-2" title="2">gmkin()</a></code></pre></div> +<p>You may also want to adapt the browser that R starts (using e.g. <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(browser="/usr/bin/firefox")</a></code> on linux, or setting the default browser on Windows).</p> </div> <div id="documentation" class="section level2"> <h2 class="hasAnchor"> @@ -137,9 +138,9 @@ <h3 class="hasAnchor"> <a href="#installation-using-the-devtools-package" class="anchor"></a>Installation using the devtools package</h3> <p>Users of the <code>devtools</code> package can also install gWidgetsWWW2 and gmkin directly from the respective github repositories:</p> -<div class="sourceCode" id="cb6"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb6-1" data-line-number="1">require(devtools)</a> -<a class="sourceLine" id="cb6-2" data-line-number="2">install_github(<span class="st">"jverzani/gWidgetsWWW2"</span>, quick = TRUE)</a> -<a class="sourceLine" id="cb6-3" data-line-number="3">install_github(<span class="st">"jranke/gmkin"</span>, quick = TRUE)</a></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb6-1" title="1">require(devtools)</a> +<a class="sourceLine" id="cb6-2" title="2">install_github(<span class="st">"jverzani/gWidgetsWWW2"</span>, quick = TRUE)</a> +<a class="sourceLine" id="cb6-3" title="3">install_github(<span class="st">"jranke/gmkin"</span>, quick = TRUE)</a></code></pre></div> <p>Installing gWidgetsWWW2 in this way yields a lot of warnings concerning overly long path names (see Notes on gWidgetsWWW2 above). Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p> </div> </div> @@ -147,11 +148,11 @@ <h2 class="hasAnchor"> <a href="#simplifying-the-start-of-gmkin-under-windows" class="anchor"></a>Simplifying the start of gmkin under Windows</h2> <p>You can put the commands</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb7-1" data-line-number="1">require(gmkin)</a> -<a class="sourceLine" id="cb7-2" data-line-number="2">gmkin()</a> -<a class="sourceLine" id="cb7-3" data-line-number="3">while (TRUE) {</a> -<a class="sourceLine" id="cb7-4" data-line-number="4"> Sys.sleep(<span class="dv">10</span>)</a> -<a class="sourceLine" id="cb7-5" data-line-number="5">}</a></code></pre></div> +<div class="sourceCode" id="cb7"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb7-1" title="1">require(gmkin)</a> +<a class="sourceLine" id="cb7-2" title="2">gmkin()</a> +<a class="sourceLine" id="cb7-3" title="3">while (TRUE) {</a> +<a class="sourceLine" id="cb7-4" title="4"> Sys.sleep(<span class="dv">10</span>)</a> +<a class="sourceLine" id="cb7-5" title="5">}</a></code></pre></div> <p>into an R script (e.g. under <code>C:\Users\<your username>\AppData\Roaming\gmkin_start.R</code>), and create a Windows shortcut, e.g. on the Desktop, with the target <code>"C:\Program Files\R\R-3.x.y\bin\R.exe" --slave -f c:\Users\<your username>\AppData\Roaming\gmkin_start.R</code>, where R.x.y is the version of R that you would like to use with gmkin. This will start a non-interactive R console that runs the gmkin GUI. In the properties dialogue of the shortcut, you can also set the working directory in which it starts gmkin. Thanks to Jonas Klein of the Umweltbundesamt for the trick with using Sys.sleep in a while loop and for suggesting the AppData directory for the start script.</p> </div> <div id="acknowledgements" class="section level2"> @@ -162,7 +163,7 @@ </div> </div> - <div class="col-md-3" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="links"> <h2>Links</h2> <ul class="list-unstyled"> @@ -187,15 +188,13 @@ </div> </div> - <footer><div class="copyright"> <p>Developed by Johannes Ranke.</p> </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> |