diff options
Diffstat (limited to 'docs')
| -rw-r--r-- | docs/articles/gmkin_manual.html | 31 | ||||
| -rw-r--r-- | docs/articles/index.html | 27 | ||||
| -rw-r--r-- | docs/authors.html | 33 | ||||
| -rw-r--r-- | docs/index.html | 38 | ||||
| -rw-r--r-- | docs/news/index.html | 27 | ||||
| -rw-r--r-- | docs/pkgdown.css | 42 | ||||
| -rw-r--r-- | docs/pkgdown.js | 88 | ||||
| -rw-r--r-- | docs/reference/FOCUS_2006.html | 44 | ||||
| -rw-r--r-- | docs/reference/FOCUS_2006_Z.html | 38 | ||||
| -rw-r--r-- | docs/reference/UBA_model_gallery.html | 33 | ||||
| -rw-r--r-- | docs/reference/gmkin.html | 62 | ||||
| -rw-r--r-- | docs/reference/gmkinws.html | 28 | ||||
| -rw-r--r-- | docs/reference/index.html | 27 |
13 files changed, 437 insertions, 81 deletions
diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html index 389ffdb..f283cf6 100644 --- a/docs/articles/gmkin_manual.html +++ b/docs/articles/gmkin_manual.html @@ -8,8 +8,11 @@ <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"> -<!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script><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]> <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]--> @@ -29,10 +32,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> <li> - <a href="../articles/index.html">Articles</a> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -53,7 +71,7 @@ <h1>Manual for gmkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2017-11-15</h4> + <h4 class="date">2018-03-01</h4> </div> @@ -351,7 +369,8 @@ Optimisation by method Port successfully terminated.</code></pre></div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div id="tocnav"> - <h2>Contents</h2> + <h2 class="hasAnchor"> +<a href="#tocnav" class="anchor"></a>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#introduction">Introduction</a></li> <li><a href="#starting-gmkin">Starting gmkin</a></li> @@ -374,7 +393,7 @@ Optimisation by method Port successfully terminated.</code></pre></div> </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/articles/index.html b/docs/articles/index.html index 20f744f..bfd24e2 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -18,12 +18,16 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Articles" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +55,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -94,7 +113,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/authors.html b/docs/authors.html index bd091af..fa7d1eb 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -18,12 +18,16 @@ <!-- 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> <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> <script src="jquery.sticky-kit.min.js"></script> <script src="pkgdown.js"></script> - + + +<meta property="og:title" content="Authors" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +55,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="reference/index.html">Reference</a> + <a href="index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="articles/index.html">Articles</a> + <a href="reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="news/index.html">News</a> @@ -79,15 +98,15 @@ <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. </p> </li> <li> - <p><strong>Stefan Meinecke</strong>. Contributor. + <p><strong>Stefan Meinecke</strong>. Contributor. </p> </li> <li> - <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. + <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. </p> </li> </ul> @@ -103,7 +122,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/index.html b/docs/index.html index a868144..1f2056b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,13 @@ <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"> -<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- 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><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script><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]> <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]--> @@ -29,10 +34,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="reference/index.html">Reference</a> </li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> <li> - <a href="articles/index.html">Articles</a> + <a href="articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="news/index.html">News</a> @@ -52,7 +72,7 @@ <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> <div id="system-requirements" class="section level2"> <h2 class="hasAnchor"> <a href="#system-requirements" class="anchor"></a>System requirements</h2> @@ -148,15 +168,9 @@ while (TRUE) { <p>GPL</p> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> <li><a href="authors.html">All authors...</a></li> </ul> -<h2>Dev status</h2> -<ul class="list-unstyled"> -<li><a href="https://pkgdown.jrwb.de/gmkin">gmkin</a></li> -<li><a href="https://pkgdown.jrwb.de/mkin">mkin</a></li> -<li><a href="http://github.com/jverzani/gWidgetsWWW2">gWidgetsWWW2</a></li> -</ul> </div> </div> @@ -166,7 +180,7 @@ while (TRUE) { </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/news/index.html b/docs/news/index.html index 77bd232..78f1749 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -18,12 +18,16 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="All news" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +55,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -98,7 +117,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9c437c7..181fe63 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -34,6 +34,10 @@ img.icon { float: right; } +img { + max-width: 100%; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -96,6 +100,11 @@ a.anchor { margin-bottom: 0.5em; } +.orcid { + height: 16px; + vertical-align: middle; +} + /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} @@ -133,15 +142,30 @@ pre, code { color: #333; } -pre img { +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { background-color: #fff; display: block; + height: auto; } code a, pre a { color: #375f84; } +a.sourceLine:hover { + text-decoration: none; +} + .fl {color: #1514b5;} .fu {color: #000000;} /* function */ .ch,.st {color: #036a07;} /* string */ @@ -152,3 +176,19 @@ code a, pre a { .error { color: orange; font-weight: bolder;} .warning { color: #6A0366; font-weight: bolder;} +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index c8b38c4..64b20df 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,8 +1,94 @@ $(function() { - $("#sidebar").stick_in_parent({offset_top: 40}); + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + $('body').scrollspy({ target: '#sidebar', offset: 60 }); + var cur_path = paths(location.pathname); + $("#navbar ul li a").each(function(index, value) { + if (value.text == "Home") + return; + if (value.getAttribute("href") === "#") + return; + + var path = paths(value.pathname); + if (is_prefix(cur_path, path)) { + // Add class to parent <li>, and enclosing <li> if in dropdown + var menu_anchor = $(value); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); }); + +function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); +} + +function is_prefix(needle, haystack) { + if (needle.length > haystack.lengh) + return(false); + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(false); + } + + return(true); +} + +/* Clipboard --------------------------*/ + +function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); +} + +if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>"; + + $(".examples").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); +} + diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html index 2c9d327..ca9b5ce 100644 --- a/docs/reference/FOCUS_2006.html +++ b/docs/reference/FOCUS_2006.html @@ -18,12 +18,21 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006" /> + +<meta property="og:description" content="An gmkinws object with data taken from FOCUS (2006), Appendix + 3. This is the the workspace that is loaded into gmkin by + default." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +60,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -96,16 +120,16 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>not_run</span>({ - <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>) - <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span> - <span class='co'># restoring the workspace that is loaded at startup.</span> + <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> + <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>) + <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span> + <span class='co'># restoring the workspace that is loaded at startup.</span> -})</div></pre> +<span class='co'># }</span></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -127,7 +151,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html index dff1b0e..4eff2a7 100644 --- a/docs/reference/FOCUS_2006_Z.html +++ b/docs/reference/FOCUS_2006_Z.html @@ -18,12 +18,19 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z" /> +<meta property="og:description" content="Data taken from FOCUS (2006), Appendix 7, p. 350." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +58,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -94,15 +116,15 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>not_run</span>({ - <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>) - <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span> + <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> + <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>) + <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span> -})</div></pre> +<span class='co'># }</span></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -124,7 +146,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html index 74fc20b..4157743 100644 --- a/docs/reference/UBA_model_gallery.html +++ b/docs/reference/UBA_model_gallery.html @@ -18,12 +18,24 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="A collection of some standard kinetic models — UBA_model_gallery" /> +<meta property="og:description" content="The UBA model gallery contains predefined kinetic models for some common use + cases, with metabolites named as in the commonly used PELMO degradation + scheme (Jene 1998). Please use the model gallery of the gmkin + GUI to see their definitions. The models use the topology of the models + defined by Michael Klein (2010) for DegKinManager, with the exception of the + kinetic sorption model." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +63,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -125,7 +152,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html index 961372e..75548cb 100644 --- a/docs/reference/gmkin.html +++ b/docs/reference/gmkin.html @@ -18,12 +18,21 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin" /> + +<meta property="og:description" content="This function starts a browser based GUI. Please visit the + github page of gWidgetsWWW2 + for an explanation how this toolkit works." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +60,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -79,7 +103,7 @@ <p>This function starts a browser based GUI. Please visit the - <a href = 'http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> + <a href='http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> for an explanation how this toolkit works.</p> @@ -107,19 +131,21 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'>## Not run: gmkin() # Start the gmkin GUI</span> - <span class='fu'>not_run</span>({ - <span class='no'>g</span> <span class='kw'><-</span> <span class='fu'>gmkin</span>() - - <span class='co'># Only for debugging or other advanced usage:</span> - <span class='no'>session</span> <span class='kw'><-</span> <span class='kw'>gmkin</span><span class='kw'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>) - <span class='no'>session</span>$<span class='no'>p.df</span> - <span class='no'>session</span>$<span class='no'>ds.df</span> - <span class='no'>session</span>$<span class='no'>ds.cur</span> - <span class='no'>session</span>$<span class='no'>m.cur</span> - <span class='no'>session</span>$<span class='no'>ws</span> - -})</div></pre> + <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> +<span class='fu'>gmkin</span>() +<span class='co'># }</span><div class='input'> # Start the gmkin GUI + </div><span class='co'># NOT RUN {</span> + <span class='no'>g</span> <span class='kw'><-</span> <span class='fu'>gmkin</span>() + + <span class='co'># Only for debugging or other advanced usage:</span> + <span class='no'>session</span> <span class='kw'><-</span> <span class='kw pkg'>gmkin</span><span class='kw ns'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>) + <span class='no'>session</span>$<span class='no'>p.df</span> + <span class='no'>session</span>$<span class='no'>ds.df</span> + <span class='no'>session</span>$<span class='no'>ds.cur</span> + <span class='no'>session</span>$<span class='no'>m.cur</span> + <span class='no'>session</span>$<span class='no'>ws</span> + +<span class='co'># }</span></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -144,7 +170,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html index 28f6014..2c1f509 100644 --- a/docs/reference/gmkinws.html +++ b/docs/reference/gmkinws.html @@ -18,12 +18,19 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="A workspace class for gmkin — gmkinws" /> +<meta property="og:description" content="Datasets, models and fits are stored in lists." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +58,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -118,7 +140,7 @@ by the names used in the models contained in field m</p></dd> </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6f21a01..3fd068b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,12 +18,16 @@ <!-- 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> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Function reference" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,10 +55,25 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Reference</a> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> </li> <li> - <a href="../articles/index.html">Articles</a> + <a href="../reference/index.html">Reference</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/gmkin_manual.html">Manual for gmkin</a> + </li> + </ul> </li> <li> <a href="../news/index.html">News</a> @@ -145,7 +164,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> |