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1 files changed, 25 insertions, 25 deletions
diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html index dc2ef4d..646b534 100644 --- a/docs/articles/gmkin_manual.html +++ b/docs/articles/gmkin_manual.html @@ -29,7 +29,7 @@ </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">0.6.8</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.9</span> </span> </div> @@ -75,7 +75,7 @@ <h1>Manual for gmkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-06-06</h4> + <h4 class="date">2018-09-13</h4> <div class="hidden name"><code>gmkin_manual.Rmd</code></div> @@ -94,11 +94,11 @@ <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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(gmkin)</code></pre></div> +<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> <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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/gmkin.html">gmkin</a></span>()</code></pre></div> +<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> <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 +160,9 @@ <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"><pre class="sourceCode r"><code class="sourceCode r"><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>, - <span class="dt">row.names =</span> <span class="ot">FALSE</span>, <span class="dt">quote =</span> <span class="ot">FALSE</span>, - <span class="dt">file =</span> <span class="st">"schaefer07.csv"</span>)</code></pre></div> +<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> <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 +241,23 @@ <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"><pre class="sourceCode r"><code class="sourceCode r">Model cost at call <span class="dv">1</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span> -Model cost at call <span class="dv">3</span> <span class="op">:</span><span class="st"> </span><span class="fl">15156.12</span> -Model cost at call <span class="dv">7</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> -Model cost at call <span class="dv">8</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> -Model cost at call <span class="dv">11</span> <span class="op">:</span><span class="st"> </span><span class="fl">14220.79</span> -Model cost at call <span class="dv">12</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span> -Model cost at call <span class="dv">15</span> <span class="op">:</span><span class="st"> </span><span class="fl">3349.268</span> -Model cost at call <span class="dv">17</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6367</span> -Model cost at call <span class="dv">18</span> <span class="op">:</span><span class="st"> </span><span class="fl">788.6366</span> -Model cost at call <span class="dv">22</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span> -Model cost at call <span class="dv">23</span> <span class="op">:</span><span class="st"> </span><span class="fl">374.0575</span> -Model cost at call <span class="dv">27</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span> -Model cost at call <span class="dv">28</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2135</span> -Model cost at call <span class="dv">32</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> -Model cost at call <span class="dv">36</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> -Model cost at call <span class="dv">37</span> <span class="op">:</span><span class="st"> </span><span class="fl">371.2134</span> -Optimisation by method Port successfully terminated.</code></pre></div> +<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> <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"> @@ -321,7 +321,7 @@ Optimisation by method Port successfully terminated.</code></pre></div> <li>Enter replicates ‘1’</li> <li>Enter observed variable ‘parent, A1’</li> <li>Press ‘Generate grid for entering kinetic data’</li> -<li>In the value column of the dataset editor, enter values ‘100’, ‘30’, ‘10’, ‘5’, ‘3’, ‘’ (nothing), ’3’, ‘8’, ‘7’, ‘5’</li> +<li>In the value column of the dataset editor, enter values ‘100’, ‘30’, ‘10’, ‘5’, ‘3’, ’’ (nothing), ‘3’, ‘8’, ‘7’, ‘5’</li> <li>Press ‘Keep changes’</li> <li>Select the ‘Model gallery’ to the right</li> <li>From the model gallery, press ‘FOMC, one met’ below the corresponding model scheme</li> |