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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 0ce7bd07..ad53126e 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -16,14 +16,27 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Reference</a>
-</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+ <a href="../reference/index.html">Function 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/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul></li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -116,16 +129,16 @@
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:20 2016
-## Date of summary: Fri Nov 4 16:56:20 2016
+## Date of fit: Fri Nov 18 16:48:11 2016
+## Date of summary: Fri Nov 18 16:48:11 2016
##
## Equations:
-## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
-## d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
+## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.661 s
+## Fitted with method Port using 153 model solutions performed in 0.638 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages
index c3c384b1..f8bbf624 100644
--- a/docs/articles/FOCUS_D_cache/html/__packages
+++ b/docs/articles/FOCUS_D_cache/html/__packages
@@ -8,3 +8,5 @@ inline
mkin
rmarkdown
knitr
+microbenchmark
+ggplot2
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index e44c1374..fc237898 100644
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+++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
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diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
index c7df3486..b0a7c26b 100644
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+++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
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index c3009e4d..8f3dbe7c 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -16,14 +16,27 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Reference</a>
-</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+ <a href="../reference/index.html">Function 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/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul></li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -63,15 +76,15 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:03 2016
-## Date of summary: Fri Nov 18 15:22:03 2016
+## Date of fit: Fri Nov 18 16:48:11 2016
+## Date of summary: Fri Nov 18 16:48:11 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.085 s
##
## Weighting: none
##
@@ -156,8 +169,8 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:04 2016
-## Date of summary: Fri Nov 18 15:22:04 2016
+## Date of fit: Fri Nov 18 16:48:12 2016
+## Date of summary: Fri Nov 18 16:48:12 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -169,7 +182,7 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.445 s
+## Fitted with method Port using 188 model solutions performed in 0.448 s
##
## Weighting: none
##
@@ -253,15 +266,15 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:05 2016
-## Date of summary: Fri Nov 18 15:22:05 2016
+## Date of fit: Fri Nov 18 16:48:13 2016
+## Date of summary: Fri Nov 18 16:48:13 2016
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.196 s
##
## Weighting: none
##
@@ -323,8 +336,8 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:06 2016
-## Date of summary: Fri Nov 18 15:22:06 2016
+## Date of fit: Fri Nov 18 16:48:14 2016
+## Date of summary: Fri Nov 18 16:48:14 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -333,7 +346,7 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.803 s
+## Fitted with method Port using 336 model solutions performed in 0.793 s
##
## Weighting: none
##
@@ -412,8 +425,8 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:07 2016
-## Date of summary: Fri Nov 18 15:22:07 2016
+## Date of fit: Fri Nov 18 16:48:15 2016
+## Date of summary: Fri Nov 18 16:48:15 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -422,7 +435,7 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.329 s
+## Fitted with method Port using 137 model solutions performed in 0.325 s
##
## Weighting: none
##
@@ -512,15 +525,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:08 2016
-## Date of summary: Fri Nov 18 15:22:08 2016
+## Date of fit: Fri Nov 18 16:48:15 2016
+## Date of summary: Fri Nov 18 16:48:16 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
##
## Weighting: none
##
@@ -572,8 +585,8 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 15:22:08 2016
-## Date of summary: Fri Nov 18 15:22:08 2016
+## Date of fit: Fri Nov 18 16:48:16 2016
+## Date of summary: Fri Nov 18 16:48:16 2016
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/FOCUS_Z.aux b/docs/articles/FOCUS_Z.aux
deleted file mode 100644
index f997f2d7..00000000
--- a/docs/articles/FOCUS_Z.aux
+++ /dev/null
@@ -1,26 +0,0 @@
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-\gdef\HyperFirstAtBeginDocument#1{#1}
-\providecommand\HyField@AuxAddToFields[1]{}
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-\citation{FOCUSkinetics2011}
-\@writefile{toc}{\contentsline {section}{\numberline {1}The data}{1}{section.1}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4}}
-\bibstyle{plainnat}
-\bibdata{references}
-\bibcite{FOCUSkinetics2011}{{1}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}}
diff --git a/docs/articles/FOCUS_Z.bbl b/docs/articles/FOCUS_Z.bbl
deleted file mode 100644
index 451497c8..00000000
--- a/docs/articles/FOCUS_Z.bbl
+++ /dev/null
@@ -1,15 +0,0 @@
-\begin{thebibliography}{1}
-\providecommand{\natexlab}[1]{#1}
-\providecommand{\url}[1]{\texttt{#1}}
-\expandafter\ifx\csname urlstyle\endcsname\relax
- \providecommand{\doi}[1]{doi: #1}\else
- \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
-
-\bibitem[{FOCUS Work Group on Degradation Kinetics}(2011)]{FOCUSkinetics2011}
-{FOCUS Work Group on Degradation Kinetics}.
-\newblock \emph{Generic guidance for estimating persistence and degradation
- kinetics from environmental fate studies on pesticides in EU registration},
- 1.0 edition, November 2011.
-\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}.
-
-\end{thebibliography}
diff --git a/docs/articles/FOCUS_Z.blg b/docs/articles/FOCUS_Z.blg
deleted file mode 100644
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diff --git a/docs/articles/FOCUS_Z.out b/docs/articles/FOCUS_Z.out
deleted file mode 100644
index 61a86d0f..00000000
--- a/docs/articles/FOCUS_Z.out
+++ /dev/null
@@ -1,4 +0,0 @@
-\BOOKMARK [1][-]{section.1}{The data}{}% 1
-\BOOKMARK [1][-]{section.2}{Parent compound and one metabolite}{}% 2
-\BOOKMARK [1][-]{section.3}{Including metabolites Z2 and Z3}{}% 3
-\BOOKMARK [1][-]{section.4}{Using the SFORB model for parent and metabolites}{}% 4
diff --git a/docs/articles/FOCUS_Z.tex b/docs/articles/FOCUS_Z.tex
deleted file mode 100644
index f1886acd..00000000
--- a/docs/articles/FOCUS_Z.tex
+++ /dev/null
@@ -1,566 +0,0 @@
-%\VignetteIndexEntry{Example evaluation of FOCUS dataset Z}
-%\VignetteEngine{knitr::knitr}
-\documentclass[12pt,a4paper]{article}\usepackage[]{graphicx}\usepackage[]{color}
-%% maxwidth is the original width if it is less than linewidth
-%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
-\makeatletter
-\def\maxwidth{ %
- \ifdim\Gin@nat@width>\linewidth
- \linewidth
- \else
- \Gin@nat@width
- \fi
-}
-\makeatother
-
-\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
-\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
-\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
-\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
-\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
-\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
-\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
-\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
-\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
-\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
-\let\hlipl\hlkwb
-
-\usepackage{framed}
-\makeatletter
-\newenvironment{kframe}{%
- \def\at@end@of@kframe{}%
- \ifinner\ifhmode%
- \def\at@end@of@kframe{\end{minipage}}%
- \begin{minipage}{\columnwidth}%
- \fi\fi%
- \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
- \colorbox{shadecolor}{##1}\hskip-\fboxsep
- % There is no \\@totalrightmargin, so:
- \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
- \MakeFramed {\advance\hsize-\width
- \@totalleftmargin\z@ \linewidth\hsize
- \@setminipage}}%
- {\par\unskip\endMakeFramed%
- \at@end@of@kframe}
-\makeatother
-
-\definecolor{shadecolor}{rgb}{.97, .97, .97}
-\definecolor{messagecolor}{rgb}{0, 0, 0}
-\definecolor{warningcolor}{rgb}{1, 0, 1}
-\definecolor{errorcolor}{rgb}{1, 0, 0}
-\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
-
-\usepackage{alltt}
-\usepackage{a4wide}
-\input{header}
-\hypersetup{
- pdftitle = {Example evaluation of FOCUS dataset Z},
- pdfsubject = {Manuscript},
- pdfauthor = {Johannes Ranke},
- colorlinks = {true},
- linkcolor = {blue},
- citecolor = {blue},
- urlcolor = {red},
- hyperindex = {true},
- linktocpage = {true},
-}
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-\begin{document}
-
-
-
-\title{Example evaluation of FOCUS dataset Z}
-\author{\textbf{Johannes Ranke} \\[0.5cm]
-%EndAName
-Wissenschaftlicher Berater\\
-Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm]
-and\\[0.5cm]
-University of Bremen\\
-}
-\maketitle
-
-\thispagestyle{empty} \setcounter{page}{0}
-
-\clearpage
-
-\tableofcontents
-
-\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
-
-\section{The data}
-
-The following code defines the example dataset from Appendix 7 to the FOCUS kinetics
-report \citep{FOCUSkinetics2011}, p.350.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{require}\hlstd{(mkin)}
-\end{alltt}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: mkin}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: minpack.lm}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: rootSolve}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: inline}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: methods}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: parallel}}\begin{alltt}
-\hlstd{LOD} \hlkwb{=} \hlnum{0.5}
-\hlstd{FOCUS_2006_Z} \hlkwb{=} \hlkwd{data.frame}\hlstd{(}
- \hlkwc{t} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{0.04}\hlstd{,} \hlnum{0.125}\hlstd{,} \hlnum{0.29}\hlstd{,} \hlnum{0.54}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{2}\hlstd{,} \hlnum{3}\hlstd{,} \hlnum{4}\hlstd{,} \hlnum{7}\hlstd{,} \hlnum{10}\hlstd{,} \hlnum{14}\hlstd{,} \hlnum{21}\hlstd{,}
- \hlnum{42}\hlstd{,} \hlnum{61}\hlstd{,} \hlnum{96}\hlstd{,} \hlnum{124}\hlstd{),}
- \hlkwc{Z0} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{100}\hlstd{,} \hlnum{81.7}\hlstd{,} \hlnum{70.4}\hlstd{,} \hlnum{51.1}\hlstd{,} \hlnum{41.2}\hlstd{,} \hlnum{6.6}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{3.9}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{4.3}\hlstd{,} \hlnum{6.8}\hlstd{,}
- \hlnum{2.9}\hlstd{,} \hlnum{3.5}\hlstd{,} \hlnum{5.3}\hlstd{,} \hlnum{4.4}\hlstd{,} \hlnum{1.2}\hlstd{,} \hlnum{0.7}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{18.3}\hlstd{,} \hlnum{29.6}\hlstd{,} \hlnum{46.3}\hlstd{,} \hlnum{55.1}\hlstd{,} \hlnum{65.7}\hlstd{,} \hlnum{39.1}\hlstd{,} \hlnum{36}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{5.6}\hlstd{,} \hlnum{1.1}\hlstd{,}
- \hlnum{1.6}\hlstd{,} \hlnum{0.6}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{2.6}\hlstd{,} \hlnum{3.8}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{37.2}\hlstd{,} \hlnum{31.7}\hlstd{,} \hlnum{35.6}\hlstd{,} \hlnum{14.5}\hlstd{,}
- \hlnum{0.8}\hlstd{,} \hlnum{2.1}\hlstd{,} \hlnum{1.9}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),}
- \hlkwc{Z3} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{9.2}\hlstd{,} \hlnum{13.1}\hlstd{,} \hlnum{22.3}\hlstd{,} \hlnum{28.4}\hlstd{,} \hlnum{32.5}\hlstd{,}
- \hlnum{25.2}\hlstd{,} \hlnum{17.2}\hlstd{,} \hlnum{4.8}\hlstd{,} \hlnum{4.5}\hlstd{,} \hlnum{2.8}\hlstd{,} \hlnum{4.4}\hlstd{))}
-
-\hlstd{FOCUS_2006_Z_mkin} \hlkwb{<-} \hlkwd{mkin_wide_to_long}\hlstd{(FOCUS_2006_Z)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-\section{Parent compound and one metabolite}
-
-The next step is to set up the models used for the kinetic analysis. As the
-simultaneous fit of parent and the first metabolite is usually straightforward,
-Step 1 (SFO for parent only) is skipped here. We start with the model 2a,
-with formation and decline of metabolite Z1 and the pathway from parent
-directly to sink included (default in mkin).
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.2a} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.2a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.2a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_1-1}
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.2a,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-## Estimate se_notrans t value Pr(>t)
-## Z0_0 9.701488e+01 3.55313691 2.730401e+01 1.679214e-21
-## k_Z0_sink 1.281376e-11 0.22689470 5.647447e-11 5.000000e-01
-## k_Z0_Z1 2.236006e+00 0.16507604 1.354531e+01 7.396594e-14
-## k_Z1_sink 4.821248e-01 0.06585369 7.321150e+00 3.552015e-08
-## Lower Upper
-## Z0_0 91.4058170 102.6239462
-## k_Z0_sink 0.0000000 Inf
-## k_Z0_Z1 1.8419826 2.7143172
-## k_Z1_sink 0.4005856 0.5802613
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-As obvious from the parameter summary (the \texttt{bpar} component of the
-summary), the kinetic rate constant from parent compound Z to sink
-is negligible. Accordingly, the exact magnitude of the fitted parameter
-\texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not
-returned (not shown, would be visible in the complete summary).
-This suggests, in agreement with the analysis in the FOCUS kinetics report, to
-simplify the model by removing the pathway to sink.
-
-A similar result can be obtained when formation fractions are used in the model
-formulation:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.2a.ff} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),}
- \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.2a.ff} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a.ff, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.2a.ff)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_2-1}
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.2a.ff,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-## Estimate se_notrans t value Pr(>t) Lower
-## Z0_0 97.0148812 3.55314944 27.303912 1.679369e-21 91.3287912
-## k_Z0 2.2360064 0.21684747 10.311425 3.661846e-11 1.8052909
-## k_Z1 0.4821248 0.06585372 7.321147 3.552045e-08 0.3996826
-## f_Z0_to_Z1 1.0000000 0.10147342 9.854798 9.707056e-11 0.0000000
-## Upper
-## Z0_0 102.7009713
-## k_Z0 2.7694843
-## k_Z1 0.5815722
-## f_Z0_to_Z1 1.0000000
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Here, the ilr transformed formation fraction fitted in the model takes a very
-large value, and the backtransformed formation fraction from parent Z to Z1 is
-practically unity. Again, the covariance matrix is not returned as the model is
-overparameterised.
-
-The simplified model is obtained by setting the list component \texttt{sink} to
-\texttt{FALSE}.\footnote{If the model formulation without formation fractions
-is used, the same effect can be obtained by fixing the parameter \texttt{k\_Z\_sink}
-to a value of zero.}
-
-In the following, we use the parameterisation with formation fractions in order
-to be able to compare with the results in the FOCUS guidance, and as it
-makes it easier to use parameters obtained in a previous fit when adding a further
-metabolite.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.3)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_3-1}
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.3,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-## Estimate se_notrans t value Pr(>t) Lower
-## Z0_0 97.0148815 2.68177093 36.17568 2.363587e-25 91.5215237
-## k_Z0 2.2360064 0.14686110 15.22531 2.246514e-15 1.9545310
-## k_Z1 0.4821248 0.04268712 11.29439 3.068581e-12 0.4021552
-## Upper
-## Z0_0 102.5082392
-## k_Z0 2.5580177
-## k_Z1 0.5779966
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-As there is only one transformation product for Z0 and no pathway
-to sink, the formation fraction is internally fixed to unity.
-
-\section{Including metabolites Z2 and Z3}
-
-As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as
-well in the next step. While this step appears questionable on the basis of the above results, it
-is followed here for the purpose of comparison. Also, in the FOCUS report, it is
-assumed that there is additional empirical evidence that Z1 quickly and exclusively
-hydrolyses to Z2.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.5, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.5)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_5-1}
-
-\end{knitrout}
-
-Finally, metabolite Z3 is added to the model. We use the optimised
-differential equation parameter values from the previous fit in order to
-accelerate the optimization.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.FOCUS} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
- \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),}
- \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.FOCUS} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.FOCUS, FOCUS_2006_Z_mkin,}
- \hlkwc{parms.ini} \hlstd{= m.Z.5}\hlopt{$}\hlstd{bparms.ode,}
- \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.FOCUS)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_6-1}
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.FOCUS,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-## Estimate se_notrans t value Pr(>t) Lower
-## Z0_0 96.83849566 2.05886133 47.034977 5.583742e-44 92.70517559
-## k_Z0 2.21540897 0.11813046 18.753919 7.744034e-25 1.99051134
-## k_Z1 0.47829896 0.02928763 16.331089 3.333376e-22 0.42297603
-## k_Z2 0.45161653 0.04421268 10.214638 3.110936e-14 0.37103495
-## k_Z3 0.05869343 0.01429485 4.105914 7.285393e-05 0.03599566
-## f_Z2_to_Z3 0.47150952 0.05705233 8.264510 2.809889e-11 0.36038193
-## Upper
-## Z0_0 100.97181573
-## k_Z0 2.46571661
-## k_Z1 0.54085782
-## k_Z2 0.54969886
-## k_Z3 0.09570371
-## f_Z2_to_Z3 0.58553462
-\end{verbatim}
-\begin{alltt}
-\hlkwd{endpoints}\hlstd{(m.Z.FOCUS)}
-\end{alltt}
-\begin{verbatim}
-## $ff
-## Z2_Z3 Z2_sink
-## 0.4715095 0.5284905
-##
-## $SFORB
-## logical(0)
-##
-## $distimes
-## DT50 DT90
-## Z0 0.3128755 1.039350
-## Z1 1.4491923 4.814113
-## Z2 1.5348136 5.098540
-## Z3 11.8096217 39.230714
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-This fit corresponds to the final result chosen in Appendix 7 of the FOCUS
-report. Confidence intervals returned by mkin are based on internally
-transformed parameters, however.
-
-\section{Using the SFORB model for parent and metabolites}
-
-As the FOCUS report states, there is a certain tailing of the time course of metabolite
-Z3. Also, the time course of the parent compound is not fitted very well using the
-SFO model, as residues at a certain low level remain.
-
-Therefore, an additional model is offered here, using the single first-order
-reversible binding (SFORB) model for metabolite Z3. As expected, the $\chi^2$
-error level is lower for metabolite Z3 using this model and the graphical
-fit for Z3 is improved. However, the covariance matrix is not returned.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.1} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
- \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.1} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.1, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.1)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_7-1}
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.mkin.1,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{cov.unscaled}
-\end{alltt}
-\begin{verbatim}
-## NULL
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Therefore, a further stepwise model building is performed starting from the
-stage of parent and two metabolites, starting from the assumption that the model
-fit for the parent compound can be improved by using the SFORB model.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.3)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_9-1}
-
-\end{knitrout}
-
-This results in a much better representation of the behaviour of the parent
-compound Z0.
-
-Finally, Z3 is added as well. These models appear overparameterised (no
-covariance matrix returned) if the sink for Z1 is left in the models.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.4} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
- \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.4} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.4, FOCUS_2006_Z_mkin,}
- \hlkwc{parms.ini} \hlstd{= m.Z.mkin.3}\hlopt{$}\hlstd{bparms.ode,}
- \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.4)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_10-1}
-
-\end{knitrout}
-
-The error level of the fit, but especially of metabolite Z3, can be improved if
-the SFORB model is chosen for this metabolite, as this model is capable of
-representing the tailing of the metabolite decline phase.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
- \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
- \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,}
- \hlkwc{parms.ini} \hlstd{= m.Z.mkin.4}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{4}\hlstd{],}
- \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11-1}
-
-\end{knitrout}
-
-The summary view of the backtransformed parameters shows that we get no
-confidence intervals due to overparameterisation. As the optimized
-\texttt{k\_Z3\_bound\_free} is excessively small, it seems reasonable to fix it to
-zero.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{m.Z.mkin.5a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,}
- \hlkwc{parms.ini} \hlstd{=} \hlkwd{c}\hlstd{(m.Z.mkin.5}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{7}\hlstd{],}
- \hlkwc{k_Z3_bound_free} \hlstd{=} \hlnum{0}\hlstd{),}
- \hlkwc{fixed_parms} \hlstd{=} \hlstr{"k_Z3_bound_free"}\hlstd{,}
- \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11a-1}
-
-\end{knitrout}
-
-As expected, the residual plots for Z0 and Z3 are more random than in the case of the
-all SFO model for which they were shown above. In conclusion, the model
-\texttt{Z.mkin.5a} is proposed as the best-fit model for the dataset from
-Appendix 7 of the FOCUS report.
-
-A graphical representation of the confidence intervals can finally be obtained.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{mkinparplot}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11b-1}
-
-\end{knitrout}
-
-The endpoints obtained with this model are
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{endpoints}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\begin{verbatim}
-## $ff
-## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink
-## 1.0000000 1.0000000 0.4634431 0.5365569 1.0000000
-##
-## $SFORB
-## Z0_b1 Z0_b2 Z3_b1 Z3_b2
-## 2.447138640 0.007512589 0.080007099 0.000000000
-##
-## $distimes
-## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3042972 1.184811 0.283248 92.26476 NA NA
-## Z1 1.5147787 5.031986 NA NA NA NA
-## Z2 1.6413857 5.452565 NA NA NA NA
-## Z3 NA NA NA NA 8.663571 Inf
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-It is clear the degradation rate of Z3 towards the end of the experiment
-is very low as DT50\_Z3\_b2 (the second Eigenvalue of the system of two differential
-equations representing the SFORB system for Z3, corresponding to the slower rate
-constant of the DFOP model) is reported to be infinity. However, this appears
-to be a feature of the data.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
diff --git a/docs/articles/FOCUS_Z.toc b/docs/articles/FOCUS_Z.toc
deleted file mode 100644
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@@ -1,4 +0,0 @@
-\contentsline {section}{\numberline {1}The data}{1}{section.1}
-\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2}
-\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3}
-\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4}
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diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages
deleted file mode 100644
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--- a/docs/articles/cache/__packages
+++ /dev/null
@@ -1,6 +0,0 @@
-base
-knitr
-minpack.lm
-rootSolve
-inline
-mkin
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index ce149bc5..31340867 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -16,14 +16,27 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Reference</a>
-</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+ <a href="../reference/index.html">Function 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/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul></li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -78,21 +91,21 @@ mb<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724
-## Eigenvalue based 907.1699 908.8498 921.8335 910.5297 929.1653
-## deSolve, compiled 747.5311 752.3718 754.2086 757.2125 757.5474
+## deSolve, not compiled 6559.0772 6574.0500 6642.0659 6589.0229 6683.5603
+## Eigenvalue based 921.0723 931.1284 940.3973 941.1845 950.0598
+## deSolve, compiled 736.6534 741.6706 756.3600 746.6878 766.2132
## max neval cld
-## 6394.1290 3 c
-## 947.8008 3 b
-## 757.8823 3 a</code></pre>
+## 6778.0978 3 c
+## 958.9351 3 b
+## 785.7386 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
-<p>We see that using the compiled model is by a factor of 8.4 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
+<p>We see that using the compiled model is by a factor of 8.8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) &lt;-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 8.433585
-## Eigenvalue based 1.202476
+## deSolve, not compiled 8.824334
+## Eigenvalue based 1.260479
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -113,19 +126,19 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>)
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
-## expr min lq mean median uq
-## deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740
-## deSolve, compiled 1.303868 1.307484 1.332879 1.311099 1.347384
+## expr min lq mean median uq
+## deSolve, not compiled 13.587184 13.616178 13.673277 13.64517 13.716324
+## deSolve, compiled 1.307508 1.317114 1.337594 1.32672 1.352637
## max neval cld
-## 13.655915 3 b
-## 1.383669 3 a</code></pre>
+## 13.787476 3 b
+## 1.378553 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10.3 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 53b631b1..b7fda1ed 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
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diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 6d78194f..bacdb814 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index cd6a7bea..de2a8a61 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,13 +49,28 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../reference/index.html">Reference</a>
+ <a href="../reference/index.html">Function reference</a>
</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+<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/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul>
</li>
</ul>
@@ -88,7 +103,7 @@
<li><a href="compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
<li><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
<li><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
- <li><a href="mkin.html">mkin - Kinetic evaluation of chemical degradation data</a></li>
+ <li><a href="mkin.html">Introduction to mkin</a></li>
</ul>
</div>
</div>
diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R
index 67dc3623..fc39bfda 100644
--- a/docs/articles/mkin.R
+++ b/docs/articles/mkin.R
@@ -2,33 +2,3 @@
require(knitr)
opts_chunk$set(engine='R', tidy=FALSE)
-## ---- echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7----
-library(mkin)
-# Define the kinetic model
-m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
- M1 = mkinsub("SFO", "M2"),
- M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
-
-
-# Produce model predictions using some arbitrary parameters
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO,
- c(k_parent = 0.03,
- f_parent_to_M1 = 0.5, k_M1 = log(2)/100,
- f_M1_to_M2 = 0.9, k_M2 = log(2)/50),
- c(parent = 100, M1 = 0, M2 = 0),
- sampling_times)
-
-# Generate a dataset by adding normally distributed errors with
-# standard deviation 3, for two replicates at each sampling time
-d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, reps = 2,
- sdfunc = function(x) 3,
- n = 1, seed = 123456789 )
-
-# Fit the model to the dataset
-f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)
-
-# Plot the results separately for parent and metabolites
-plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))
-
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 8134287b..49c0389b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>mkin - Kinetic evaluation of chemical degradation data &bull; mkin</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://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Introduction to mkin &bull; mkin</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://cdn.mathjax.org/mathjax/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]--></head><body>
@@ -16,14 +16,27 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Reference</a>
-</li>
-<li>
- <a href="../articles/index.html">Articles</a>
-</li>
-<li>
- <a href="../news/index.html">News</a>
+ <a href="../reference/index.html">Function 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/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ </ul></li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -38,7 +51,7 @@
</header><div class="row">
<div class="col-md-9">
<div class="page-header toc-ignore">
- <h1>mkin - Kinetic evaluation of chemical degradation data</h1>
+ <h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
<h4 class="date">2016-11-18</h4>
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index ae46e2d7..ff62e6df 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -8,3 +8,5 @@ colorout
setwidth
nvimcom
rmarkdown
+microbenchmark
+ggplot2
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deleted file mode 100644
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deleted file mode 100644
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