From 0b677308e3ffbf742880f05cc54da469f3ecc854 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 9 Mar 2018 23:14:39 +0100
Subject: Another rebuild of the static docs

Now with rbenchmark installed, to get results for the compiled_models
vignette
---
 docs/index.html | 29 ++++++++++-------------------
 1 file changed, 10 insertions(+), 19 deletions(-)

(limited to 'docs/index.html')

diff --git a/docs/index.html b/docs/index.html
index c20d124b..88fd4f6d 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,17 +9,7 @@
 <!-- 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">
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-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Kinetic Evaluation of Chemical Degradation Data">
-<meta property="og:description" content="Calculation routines based on the FOCUS Kinetics Report (2006,
-  2014).  Includes a function for conveniently defining differential equation
-  models, model solution based on eigenvalues if possible or using numerical
-  solvers and a choice of the optimisation methods made available by the 'FME'
-  package.  If a C compiler (on windows: 'Rtools') is installed, differential
-  equation models are solved using compiled C functions.  Please note that no
-  warranty is implied for correctness of results or fitness for a particular
-  purpose.">
-<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="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]>
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@@ -102,7 +92,7 @@
 <div id="usage" class="section level2">
 <h2 class="hasAnchor">
 <a href="#usage" class="anchor"></a>Usage</h2>
-<p>For a start, have a look a the code examples provided for <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p>
+<p>For a start, have a look a the code examples provided for <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p>
 </div>
 <div id="documentation" class="section level2">
 <h2 class="hasAnchor">
@@ -113,17 +103,17 @@
 <h2 class="hasAnchor">
 <a href="#features" class="anchor"></a>Features</h2>
 <ul>
-<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order 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/reference/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/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
-<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/compiled_models.html">vignette <code>compiled_models</code></a>. 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>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li>
+<li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order 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="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
+<li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
+<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/compiled_models.html">vignette <code>compiled_models</code></a>. 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>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li>
 <li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li>
 <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li>
 <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li>
 <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li>
 <li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight.method = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li>
-<li>Iterative reweighting is also possible using the two-component error model for analytical data of <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/sigma_rl.html">Rocke and Lorenzato</a> using the argument <code>reweight.method = "tc"</code>.</li>
+<li>Iterative reweighting is also possible using the two-component error model for analytical data of <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_rl.html">Rocke and Lorenzato</a> using the argument <code>reweight.method = "tc"</code>.</li>
 <li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li>
 </ul>
 </div>
@@ -169,7 +159,8 @@
 <p>GPL</p>
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <br><small>(0000-0003-4371-6538)</small>
+</li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
 <h2>Dev status</h2>
-- 
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