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authorJohannes Ranke <jranke@uni-bremen.de>2015-12-09 10:20:50 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2015-12-09 10:20:50 +0100
commit556598ba543cf655cdc0a6995cc579327f9540ad (patch)
tree42c184c0b52d557272dca4a3d4a9ce80a4f60a06 /inst/web/index.html
parent9097b8ba10660034a3672a367eab9d6e11505310 (diff)
Static documentation rebuilt by staticdocs::build_site()
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@@ -66,15 +66,6 @@ if several compartments are involved.</p>
<pre><code class="r">install.packages(&quot;mkin&quot;)
</code></pre>
-<p>If looking for the latest features, you can install directly from
-<a href="http://github.com/jranke/mkin">github</a>, e.g. using the <code>devtools</code> package.
-Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and
-vignettes, to make installation as fast and painless as possible.</p>
-
-<pre><code class="r">require(devtools)
-install_github(&quot;jranke/mkin&quot;, quick = TRUE)
-</code></pre>
-
<h2>Background</h2>
<p>In the regulatory evaluation of chemical substances like plant protection
@@ -108,7 +99,7 @@ reversible binding (SFORB) model, which will automatically create
two latent state variables for the observed variable.</li>
<li>As of version 0.9-39, fitting of several models to several datasets, optionally in
parallel, is supported, see for example
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a> </li>
+<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
<li>Model solution (forward modelling) in the function
<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a>
is performed either using the analytical solution for the case of
@@ -121,10 +112,6 @@ generated C code, see<br/>
The autogeneration of C code was
inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks
to Karline Soetaert for her work on that.</li>
-<li>Model optimisation with
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html"><code>mkinfit</code></a>
-internally using the <code>modFit</code> function from the <code>FME</code> package,
-but using the Port routine <code>nlminb</code> per default.</li>
<li>By default, kinetic rate constants and kinetic formation fractions are
transformed internally using
<a href="http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html"><code>transform_odeparms</code></a>
@@ -152,9 +139,7 @@ as in KinGUII and CAKE (see below). Simply add the argument
componenent for each of the observed variables will be optimised
in a second stage after the primary optimisation algorithm has converged.</li>
<li>When a metabolite decline phase is not described well by SFO kinetics,
-either IORE kinetics (often producing failures of the integration algorithm)
-or SFORB kinetics (working nicely) can be used for the metabolite, adding one
-respectively two parameters to the system.</li>
+SFORB kinetics can be used for the metabolite.</li>
</ul>
<h2>GUI</h2>
@@ -171,9 +156,8 @@ and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">git
<h2>Credits and historical remarks</h2>
<p><code>mkin</code> would not be possible without the underlying software stack consisting
-of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a>,
-<a href="http://cran.r-project.org/package=minpack.lm">minpack.lm</a> and
-<a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p>
+of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a>
+and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p>
<p>It could not have been written without me being introduced to regulatory fate
modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories
@@ -187,7 +171,7 @@ as detailed in their guidance document from 2006, slightly updated in 2011 and
BayerCropScience, which is based on the MatLab runtime environment.</p>
<p>The companion package
-<a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> was
+<a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was
<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=2">started in 2008</a> and
<a href="http://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on
CRAN on 01 May 2010.</p>

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