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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-01 08:05:45 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-01 08:05:45 +0100
commitb372baf353b693198a4d8417cf008d04f44dd14a (patch)
treeeecbab23a30324caabf631265fd6e02ec6788fd0 /docs/reference
parent7bf092042cf850ab88dbf678bf9724b763a5bb57 (diff)
Static documentation rebuilt by current pkgdown
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/FOCUS_2006.html44
-rw-r--r--docs/reference/FOCUS_2006_Z.html38
-rw-r--r--docs/reference/UBA_model_gallery.html33
-rw-r--r--docs/reference/gmkin.html62
-rw-r--r--docs/reference/gmkinws.html28
-rw-r--r--docs/reference/index.html27
6 files changed, 186 insertions, 46 deletions
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&#8221; 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&#8221; 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'>&lt;-</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'>&lt;-</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>$<span class='no'>ws</span>
-
-})</div></pre>
+ <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span>
+<span class='fu'>gmkin</span>()
+<span class='co'># }</span><div class='input'> # Start the gmkin GUI
+ </div><span class='co'># NOT RUN {</span>
+ <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
+
+ <span class='co'># Only for debugging or other advanced usage:</span>
+ <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>gmkin</span><span class='kw ns'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
+ <span class='no'>session</span>$<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>

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