aboutsummaryrefslogtreecommitdiff
path: root/vignettes
diff options
context:
space:
mode:
authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-16 21:15:52 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-16 21:15:52 +0000
commit329dadc5fd557cbeec0d1f3a6db57b6b4d6f41d4 (patch)
tree8159a9ba673fc6c150a92748e142697c845ece1d /vignettes
parente6ba7af29db678ef437e7f8301299ec18f4c66a4 (diff)
- Some maintenance fixes
- Start of the examples vignette git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@61 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/examples-L1_SFO_plot.pdfbin0 -> 5472 bytes
-rw-r--r--vignettes/examples-L1_SFO_plots.pdfbin0 -> 6265 bytes
-rw-r--r--vignettes/examples-L1_SFO_residuals.pdfbin0 -> 4646 bytes
-rw-r--r--vignettes/examples-L2_DFOP.pdfbin0 -> 5062 bytes
-rw-r--r--vignettes/examples-L2_DFOP_2.pdfbin0 -> 5289 bytes
-rw-r--r--vignettes/examples-L2_FOMC.pdfbin0 -> 5333 bytes
-rw-r--r--vignettes/examples-L2_SFO_plot.pdfbin0 -> 5200 bytes
-rw-r--r--vignettes/examples-L2_SFO_residuals.pdfbin0 -> 4602 bytes
-rw-r--r--vignettes/examples-L3_DFOP.pdfbin0 -> 5407 bytes
-rw-r--r--vignettes/examples-L3_FOMC.pdfbin0 -> 5384 bytes
-rw-r--r--vignettes/examples-L3_SFO.pdfbin0 -> 5407 bytes
-rw-r--r--vignettes/examples-L4_FOMC.pdfbin0 -> 5403 bytes
-rw-r--r--vignettes/examples-L4_SFO.pdfbin0 -> 5405 bytes
-rw-r--r--vignettes/examples.Rnw289
-rw-r--r--vignettes/examples.aux29
-rw-r--r--vignettes/examples.bbl29
-rw-r--r--vignettes/examples.blg46
-rw-r--r--vignettes/examples.log944
-rw-r--r--vignettes/examples.out5
-rw-r--r--vignettes/examples.pdfbin0 -> 184683 bytes
-rw-r--r--vignettes/examples.tex700
-rw-r--r--vignettes/examples.toc5
22 files changed, 2047 insertions, 0 deletions
diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf
new file mode 100644
index 00000000..d4f88349
--- /dev/null
+++ b/vignettes/examples-L1_SFO_plot.pdf
Binary files differ
diff --git a/vignettes/examples-L1_SFO_plots.pdf b/vignettes/examples-L1_SFO_plots.pdf
new file mode 100644
index 00000000..d34116fe
--- /dev/null
+++ b/vignettes/examples-L1_SFO_plots.pdf
Binary files differ
diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf
new file mode 100644
index 00000000..35907df8
--- /dev/null
+++ b/vignettes/examples-L1_SFO_residuals.pdf
Binary files differ
diff --git a/vignettes/examples-L2_DFOP.pdf b/vignettes/examples-L2_DFOP.pdf
new file mode 100644
index 00000000..8bbfdf60
--- /dev/null
+++ b/vignettes/examples-L2_DFOP.pdf
Binary files differ
diff --git a/vignettes/examples-L2_DFOP_2.pdf b/vignettes/examples-L2_DFOP_2.pdf
new file mode 100644
index 00000000..3437f5da
--- /dev/null
+++ b/vignettes/examples-L2_DFOP_2.pdf
Binary files differ
diff --git a/vignettes/examples-L2_FOMC.pdf b/vignettes/examples-L2_FOMC.pdf
new file mode 100644
index 00000000..763d6175
--- /dev/null
+++ b/vignettes/examples-L2_FOMC.pdf
Binary files differ
diff --git a/vignettes/examples-L2_SFO_plot.pdf b/vignettes/examples-L2_SFO_plot.pdf
new file mode 100644
index 00000000..c8831b91
--- /dev/null
+++ b/vignettes/examples-L2_SFO_plot.pdf
Binary files differ
diff --git a/vignettes/examples-L2_SFO_residuals.pdf b/vignettes/examples-L2_SFO_residuals.pdf
new file mode 100644
index 00000000..d56b0d18
--- /dev/null
+++ b/vignettes/examples-L2_SFO_residuals.pdf
Binary files differ
diff --git a/vignettes/examples-L3_DFOP.pdf b/vignettes/examples-L3_DFOP.pdf
new file mode 100644
index 00000000..c747d793
--- /dev/null
+++ b/vignettes/examples-L3_DFOP.pdf
Binary files differ
diff --git a/vignettes/examples-L3_FOMC.pdf b/vignettes/examples-L3_FOMC.pdf
new file mode 100644
index 00000000..322dbeb0
--- /dev/null
+++ b/vignettes/examples-L3_FOMC.pdf
Binary files differ
diff --git a/vignettes/examples-L3_SFO.pdf b/vignettes/examples-L3_SFO.pdf
new file mode 100644
index 00000000..7057333b
--- /dev/null
+++ b/vignettes/examples-L3_SFO.pdf
Binary files differ
diff --git a/vignettes/examples-L4_FOMC.pdf b/vignettes/examples-L4_FOMC.pdf
new file mode 100644
index 00000000..3f164e79
--- /dev/null
+++ b/vignettes/examples-L4_FOMC.pdf
Binary files differ
diff --git a/vignettes/examples-L4_SFO.pdf b/vignettes/examples-L4_SFO.pdf
new file mode 100644
index 00000000..42cdf341
--- /dev/null
+++ b/vignettes/examples-L4_SFO.pdf
Binary files differ
diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw
new file mode 100644
index 00000000..24e1b57c
--- /dev/null
+++ b/vignettes/examples.Rnw
@@ -0,0 +1,289 @@
+% $Id: examples.Rnw 66 2010-09-03 08:50:26Z jranke $
+%%\VignetteIndexEntry{Examples for kinetic evaluations using mkin}
+%%VignetteDepends{FME}
+%%\usepackage{Sweave}
+\documentclass[12pt,a4paper]{article}
+\usepackage{a4wide}
+%%\usepackage[lists,heads]{endfloat}
+\input{header}
+\hypersetup{
+ pdftitle = {Examples for kinetic evaluations using mkin},
+ pdfsubject = {Manuscript},
+ pdfauthor = {Johannes Ranke},
+ colorlinks = {true},
+ linkcolor = {blue},
+ citecolor = {blue},
+ urlcolor = {red},
+ hyperindex = {true},
+ linktocpage = {true},
+}
+\SweaveOpts{engine=R, eps=FALSE, keep.source = TRUE}
+<<setup, echo = FALSE, results = hide>>=
+options(prompt = "R> ")
+options(SweaveHooks = list(
+ cex = function() par(cex.lab = 1.3, cex.axis = 1.3)))
+@
+\begin{document}
+\title{Examples for kinetic evaluations using mkin}
+\author{\textbf{Johannes Ranke} \\[0.5cm]
+%EndAName
+Eurofins Regulatory AG\\
+Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm]
+and\\[0.5cm]
+University of Bremen\\
+}
+\maketitle
+
+%\begin{abstract}
+%\end{abstract}
+
+
+\thispagestyle{empty} \setcounter{page}{0}
+
+\clearpage
+
+\tableofcontents
+
+\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
+
+\section{Kinetic evaluations for parent compounds}
+\label{intro}
+
+These examples are also evaluated in a parallel vignette of the
+\Rpackage{kinfit} package \citep{pkg:kinfit}. The datasets are from Appendix 3,
+of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}.
+
+\subsection{Laboratory Data L1}
+
+The following code defines example dataset L1 from the FOCUS kinetics
+report, p. 284
+
+<<FOCUS_2006_L1_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L1 = data.frame(
+ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
+ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
+ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
+ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
+FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
+@
+
+The next step is to set up the models used for the kinetic analysis. Note that
+the model definitions contain the names of the observed variables in the data.
+In this case, there is only one variable called \Robject{parent}.
+
+<<Simple_models, echo=TRUE>>=
+SFO <- mkinmod(parent = list(type = "SFO"))
+FOMC <- mkinmod(parent = list(type = "FOMC"))
+DFOP <- mkinmod(parent = list(type = "DFOP"))
+@
+
+The three models cover the first assumption of simple first order (SFO),
+the case of declining rate constant over time (FOMC) and the case of two
+different phases of the kinetics (DFOP). For a more detailed discussion
+of the models, please see the FOCUS kinetics report.
+
+The following two lines fit the model and produce the summary report
+of the model fit. This covers the numerical analysis given in the
+FOCUS report.
+
+<<L1_SFO, echo=TRUE>>=
+m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
+summary(m.L1.SFO)
+@
+
+A plot of the fit is obtained with the plot function for mkinfit objects.
+
+<<L1_SFO_plot, fig=TRUE, echo=TRUE>>=
+plot(m.L1.SFO)
+@
+
+The residual plot can be easily obtained by
+
+<<L1_SFO_residuals, fig=TRUE, echo=TRUE>>=
+mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
+@
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+<<L1_FOMC, echo=TRUE>>=
+m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
+s.m.L1.FOMC <- summary(m.L1.FOMC)
+s.m.L1.FOMC$errmin
+@
+
+Due to the higher number of parameters, and the lower number of degrees of freedom
+of the fit, the $\chi^2$ error level is actually higher for the FOMC model (3.6\%) than
+for the SFO model (3.4\%).
+
+\subsection{Laboratory Data L2}
+
+The following code defines example dataset L2 from the FOCUS kinetics
+report, p. 287
+
+<<FOCUS_2006_L2_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L2 = data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
+ parent = c(96.1, 91.8, 41.4, 38.7,
+ 19.3, 22.3, 4.6, 4.6,
+ 2.6, 1.2, 0.3, 0.6))
+FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
+@
+
+Again, the SFO model is fitted and a summary is obtained.
+
+<<L2_SFO, echo=TRUE>>=
+m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
+summary(m.L2.SFO)
+@
+
+The $\chi^2$ error level of 14\% suggests that the model does not fit very well.
+This is also obvious from the plots of the fit and the residuals.
+
+<<L2_SFO_plot, fig=TRUE, echo=TRUE>>=
+plot(m.L2.SFO)
+@
+
+In the FOCUS kinetics report, it is stated that there is no apparent systematic
+error observed from the residual plot up to the measured DT90 (approximately at
+day 5), and there is an underestimation beyond that point.
+
+<<L2_SFO_residuals, fig=TRUE, echo=TRUE>>=
+mkinresplot(m.L2.SFO, ylab = "Observed", xlab = "Time")
+@
+
+We may add that it is difficult to judge the random nature of the residuals just
+from the three samplings at days 0, 1 and 3. Also, it is not clear why a
+consistent underestimation after the approximate DT90 should be irrelevant.
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+<<L2_FOMC, echo=TRUE, fig=TRUE>>=
+m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet=TRUE)
+plot(m.L2.FOMC)
+s.m.L2.FOMC <- summary(m.L2.FOMC)
+s.m.L2.FOMC$errmin
+@
+
+The error level at which the $\chi^2$ test passes is much lower in this case.
+Therefore, the FOMC model provides a better description of the data, as less
+experimental error has to be assumed in order to explain the data.
+
+Fitting the four parameter DFOP model does not further reduce the
+$\chi^2$ error level.
+
+<<L2_DFOP, echo=TRUE, fig=TRUE>>=
+m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet=TRUE)
+plot(m.L2.DFOP)
+@
+
+Here, the default starting parameters for the DFOP model obviously do not lead
+to a reasonable solution. Therefore the fit is repeated with different starting
+parameters.
+
+<<L2_DFOP_2, echo=TRUE, fig=TRUE>>=
+m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
+ parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
+ quiet=TRUE)
+plot(m.L2.DFOP)
+summary(m.L2.DFOP)
+s.m.L2.DFOP <- summary(m.L2.DFOP)
+s.m.L2.DFOP$errmin
+@
+
+Therefore, the FOMC model is clearly the best-fit model based on the
+$\chi^2$ error level criterion.
+
+\subsection{Laboratory Data L3}
+
+The following code defines example dataset L3 from the FOCUS kinetics
+report, p. 290
+
+<<FOCUS_2006_L3_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L3 = data.frame(
+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
+ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
+FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
+@
+
+SFO model, summary and plot:
+
+<<L3_SFO, echo=TRUE, fig=TRUE>>=
+m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet=TRUE)
+summary(m.L3.SFO)
+plot(m.L3.SFO)
+@
+
+The $\chi^2$ error level of 22\% as well as the plot suggest that the model
+does not fit very well.
+
+The FOMC model performs better:
+
+<<L3_FOMC, echo=TRUE, fig=TRUE>>=
+m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet=TRUE)
+plot(m.L3.FOMC)
+s.m.L3.FOMC <- summary(m.L3.FOMC)
+s.m.L3.FOMC$errmin
+endpoints(m.L3.FOMC)
+@
+
+The error level at which the $\chi^2$ test passes is 7\% in this case.
+
+Fitting the four parameter DFOP model further reduces the $\chi^2$ error level
+considerably:
+
+<<L3_DFOP, echo=TRUE, fig=TRUE>>=
+m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet=TRUE)
+plot(m.L3.DFOP)
+s.m.L3.DFOP <- summary(m.L3.DFOP)
+s.m.L3.DFOP$errmin
+@
+
+Therefore, the DFOP model is the best-fit model based on the $\chi^2$ error
+level criterion for laboratory data L3.
+
+\subsection{Laboratory Data L4}
+
+The following code defines example dataset L4 from the FOCUS kinetics
+report, p. 293
+
+<<FOCUS_2006_L4_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L4 = data.frame(
+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
+ parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
+FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
+@
+
+SFO model, summary and plot:
+
+<<L4_SFO, echo=TRUE, fig=TRUE>>=
+m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet=TRUE)
+summary(m.L4.SFO)
+plot(m.L4.SFO)
+@
+
+The $\chi^2$ error level of 3.3\% as well as the plot suggest that the model
+fits very well.
+
+The FOMC model for comparison
+
+<<L4_FOMC, echo=TRUE, fig=TRUE>>=
+m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet=TRUE)
+plot(m.L4.FOMC)
+s.m.L4.FOMC <- summary(m.L4.FOMC)
+s.m.L4.FOMC$errmin
+@
+
+The error level at which the $\chi^2$ test passes is slightly lower for the FOMC
+model. However, the difference appears negligible.
+
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+\end{document}
+% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.aux b/vignettes/examples.aux
new file mode 100644
index 00000000..37703381
--- /dev/null
+++ b/vignettes/examples.aux
@@ -0,0 +1,29 @@
+\relax
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\citation{pkg:kinfit}
+\citation{FOCUS2006,FOCUSkinetics2011}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Kinetic evaluations for parent compounds}{1}{section.1}}
+\newlabel{intro}{{1}{1}{Kinetic evaluations for parent compounds\relax }{section.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Laboratory Data L1}{1}{subsection.1.1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Laboratory Data L2}{6}{subsection.1.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{14}{subsection.1.3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{20}{subsection.1.4}}
+\bibstyle{plainnat}
+\bibdata{references}
+\bibcite{FOCUS2006}{{1}{2006}{{FOCUS Work Group on Degradation Kinetics}}{{}}}
+\bibcite{FOCUSkinetics2011}{{2}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}}
+\bibcite{pkg:kinfit}{{3}{2012}{{Ranke}}{{}}}
diff --git a/vignettes/examples.bbl b/vignettes/examples.bbl
new file mode 100644
index 00000000..3f240cf1
--- /dev/null
+++ b/vignettes/examples.bbl
@@ -0,0 +1,29 @@
+\begin{thebibliography}{3}
+\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}(2006)]{FOCUS2006}
+{FOCUS Work Group on Degradation Kinetics}.
+\newblock \emph{Guidance Document on Estimating Persistence and Degradation
+ Kinetics from Environmental Fate Studies on Pesticides in EU Registration.
+ Report of the FOCUS Work Group on Degradation Kinetics}, 2006.
+\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}.
+\newblock EC Document Reference Sanco/10058/2005 version 2.0.
+
+\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}.
+
+\bibitem[Ranke(2012)]{pkg:kinfit}
+Johannes Ranke.
+\newblock \emph{kinfit: {R}outines for fitting simple kinetic models to
+ chemical degradation data}, 2012.
+\newblock URL \url{http://CRAN.R-project.org}.
+
+\end{thebibliography}
diff --git a/vignettes/examples.blg b/vignettes/examples.blg
new file mode 100644
index 00000000..61ca3d2c
--- /dev/null
+++ b/vignettes/examples.blg
@@ -0,0 +1,46 @@
+This is BibTeX, Version 0.99d (TeX Live 2012/Debian)
+Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
+The top-level auxiliary file: examples.aux
+The style file: plainnat.bst
+Database file #1: references.bib
+You've used 3 entries,
+ 2773 wiz_defined-function locations,
+ 609 strings with 5481 characters,
+and the built_in function-call counts, 895 in all, are:
+= -- 82
+> -- 30
+< -- 3
++ -- 12
+- -- 9
+* -- 57
+:= -- 151
+add.period$ -- 10
+call.type$ -- 3
+change.case$ -- 10
+chr.to.int$ -- 3
+cite$ -- 6
+duplicate$ -- 51
+empty$ -- 76
+format.name$ -- 12
+if$ -- 173
+int.to.chr$ -- 1
+int.to.str$ -- 1
+missing$ -- 0
+newline$ -- 24
+num.names$ -- 12
+pop$ -- 19
+preamble$ -- 1
+purify$ -- 9
+quote$ -- 0
+skip$ -- 39
+stack$ -- 0
+substring$ -- 6
+swap$ -- 7
+text.length$ -- 0
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 33
+warning$ -- 0
+while$ -- 9
+width$ -- 0
+write$ -- 46
diff --git a/vignettes/examples.log b/vignettes/examples.log
new file mode 100644
index 00000000..c1362041
--- /dev/null
+++ b/vignettes/examples.log
@@ -0,0 +1,944 @@
+This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) (format=pdflatex 2012.11.5) 16 FEB 2013 21:38
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**examples.tex
+(./examples.tex
+LaTeX2e <2011/06/27>
+Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ng
+erman, german, swissgerman, ngerman-x-2012-05-30, german-x-2012-05-30, loaded.
+(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
+Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
+(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo
+File: size12.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
+)
+\c@part=\count79
+\c@section=\count80
+\c@subsection=\count81
+\c@subsubsection=\count82
+\c@paragraph=\count83
+\c@subparagraph=\count84
+\c@figure=\count85
+\c@table=\count86
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+)
+(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
+Package: a4wide 1994/08/30
+
+(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty
+Package: a4 2004/04/15 v1.2g A4 based page layout
+)) (./header.tex
+(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty
+Package: booktabs 2005/04/14 v1.61803 publication quality tables
+\heavyrulewidth=\dimen103
+\lightrulewidth=\dimen104
+\cmidrulewidth=\dimen105
+\belowrulesep=\dimen106
+\belowbottomsep=\dimen107
+\aboverulesep=\dimen108
+\abovetopsep=\dimen109
+\cmidrulesep=\dimen110
+\cmidrulekern=\dimen111
+\defaultaddspace=\dimen112
+\@cmidla=\count87
+\@cmidlb=\count88
+\@aboverulesep=\dimen113
+\@belowrulesep=\dimen114
+\@thisruleclass=\count89
+\@lastruleclass=\count90
+\@thisrulewidth=\dimen115
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty
+Package: amsfonts 2009/06/22 v3.00 Basic AMSFonts support
+\@emptytoks=\toks14
+\symAMSa=\mathgroup4
+\symAMSb=\mathgroup5
+LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold'
+(Font) U/euf/m/n --> U/euf/b/n on input line 96.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty
+Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols)
+\symlasy=\mathgroup6
+LaTeX Font Info: Overwriting symbol font `lasy' in version `bold'
+(Font) U/lasy/m/n --> U/lasy/b/n on input line 47.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
+Package: amsmath 2000/07/18 v2.13 AMS math features
+\@mathmargin=\skip43
+
+For additional information on amsmath, use the `?' option.
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
+Package: amstext 2000/06/29 v2.01
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty
+File: amsgen.sty 1999/11/30 v2.0
+\@emptytoks=\toks15
+\ex@=\dimen116
+))
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty
+Package: amsbsy 1999/11/29 v1.2d
+\pmbraise@=\dimen117
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty
+Package: amsopn 1999/12/14 v2.01 operator names
+)
+\inf@bad=\count91
+LaTeX Info: Redefining \frac on input line 211.
+\uproot@=\count92
+\leftroot@=\count93
+LaTeX Info: Redefining \overline on input line 307.
+\classnum@=\count94
+\DOTSCASE@=\count95
+LaTeX Info: Redefining \ldots on input line 379.
+LaTeX Info: Redefining \dots on input line 382.
+LaTeX Info: Redefining \cdots on input line 467.
+\Mathstrutbox@=\box26
+\strutbox@=\box27
+\big@size=\dimen118
+LaTeX Font Info: Redeclaring font encoding OML on input line 567.
+LaTeX Font Info: Redeclaring font encoding OMS on input line 568.
+\macc@depth=\count96
+\c@MaxMatrixCols=\count97
+\dotsspace@=\muskip10
+\c@parentequation=\count98
+\dspbrk@lvl=\count99
+\tag@help=\toks16
+\row@=\count100
+\column@=\count101
+\maxfields@=\count102
+\andhelp@=\toks17
+\eqnshift@=\dimen119
+\alignsep@=\dimen120
+\tagshift@=\dimen121
+\tagwidth@=\dimen122
+\totwidth@=\dimen123
+\lineht@=\dimen124
+\@envbody=\toks18
+\multlinegap=\skip44
+\multlinetaggap=\skip45
+\mathdisplay@stack=\toks19
+LaTeX Info: Redefining \[ on input line 2666.
+LaTeX Info: Redefining \] on input line 2667.
+)
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
+Package: amssymb 2009/06/22 v3.00
+)
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
+Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV@toks@=\toks20
+)
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
+Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty
+Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
+)
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg
+File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
+)
+Package graphics Info: Driver file: pdftex.def on input line 91.
+
+(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
+File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty
+Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO)
+)
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
+Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
+)
+\Gread@gobject=\count103
+))
+\Gin@req@height=\dimen125
+\Gin@req@width=\dimen126
+)
+(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty
+Package: parskip 2001/04/09 non-zero parskip adjustments
+)
+(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty
+Package: natbib 2010/09/13 8.31b (PWD, AO)
+\bibhang=\skip46
+\bibsep=\skip47
+LaTeX Info: Redefining \cite on input line 694.
+\c@NAT@ctr=\count104
+)
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
+Package: hyperref 2012/05/13 v6.82q Hypertext links for LaTeX
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
+Package: hobsub-hyperref 2012/05/28 v1.13 Bundle oberdiek, subset hyperref (HO)
+
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty
+Package: hobsub-generic 2012/05/28 v1.13 Bundle oberdiek, subset generic (HO)
+Package: hobsub 2012/05/28 v1.13 Construct package bundles (HO)
+Package hobsub Info: Skipping package `infwarerr' (already loaded).
+Package hobsub Info: Skipping package `ltxcmds' (already loaded).
+Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
+Package ifluatex Info: LuaTeX not detected.
+Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
+Package ifvtex Info: VTeX not detected.
+Package: intcalc 2007/09/27 v1.1 Expandable calculations with integers (HO)
+Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
+Package ifpdf Info: pdfTeX in PDF mode is detected.
+Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
+Package etexcmds Info: Could not find \expanded.
+(etexcmds) That can mean that you are not using pdfTeX 1.50 or
+(etexcmds) that some package has redefined \expanded.
+(etexcmds) In the latter case, load this package earlier.
+Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)
+Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
+Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO
+)
+Package pdftexcmds Info: LuaTeX not detected.
+Package pdftexcmds Info: \pdf@primitive is available.
+Package pdftexcmds Info: \pdf@ifprimitive is available.
+Package pdftexcmds Info: \pdfdraftmode found.
+Package: pdfescape 2011/11/25 v1.13 Implements pdfTeX's escape features (HO)
+Package: bigintcalc 2012/04/08 v1.3 Expandable calculations on big integers (HO
+)
+Package: bitset 2011/01/30 v1.1 Handle bit-vector datatype (HO)
+Package: uniquecounter 2011/01/30 v1.2 Provide unlimited unique counter (HO)
+)
+Package hobsub Info: Skipping package `hobsub' (already loaded).
+Package: letltxmacro 2010/09/02 v1.4 Let assignment for LaTeX macros (HO)
+Package: hopatch 2012/05/28 v1.2 Wrapper for package hooks (HO)
+Package: xcolor-patch 2011/01/30 xcolor patch
+Package: atveryend 2011/06/30 v1.8 Hooks at the very end of document (HO)
+Package atveryend Info: \enddocument detected (standard20110627).
+Package: atbegshi 2011/10/05 v1.16 At begin shipout hook (HO)
+Package: refcount 2011/10/16 v3.4 Data extraction from label references (HO)
+Package: hycolor 2011/01/30 v1.7 Color options for hyperref/bookmark (HO)
+)
+(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty
+Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
+)
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
+Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)
+)
+\@linkdim=\dimen127
+\Hy@linkcounter=\count105
+\Hy@pagecounter=\count106
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def
+File: pd1enc.def 2012/05/13 v6.82q Hyperref: PDFDocEncoding definition (HO)
+)
+\Hy@SavedSpaceFactor=\count107
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg
+File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
+)
+Package hyperref Info: Hyper figures OFF on input line 4062.
+Package hyperref Info: Link nesting OFF on input line 4067.
+Package hyperref Info: Hyper index ON on input line 4070.
+Package hyperref Info: Plain pages OFF on input line 4077.
+Package hyperref Info: Backreferencing OFF on input line 4082.
+Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
+Package hyperref Info: Bookmarks ON on input line 4300.
+\c@Hy@tempcnt=\count108
+
+(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty
+\Urlmuskip=\muskip11
+Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.
+)
+LaTeX Info: Redefining \url on input line 4653.
+\Fld@menulength=\count109
+\Field@Width=\dimen128
+\Fld@charsize=\dimen129
+Package hyperref Info: Hyper figures OFF on input line 5773.
+Package hyperref Info: Link nesting OFF on input line 5778.
+Package hyperref Info: Hyper index ON on input line 5781.
+Package hyperref Info: backreferencing OFF on input line 5788.
+Package hyperref Info: Link coloring OFF on input line 5793.
+Package hyperref Info: Link coloring with OCG OFF on input line 5798.
+Package hyperref Info: PDF/A mode OFF on input line 5803.
+LaTeX Info: Redefining \ref on input line 5843.
+LaTeX Info: Redefining \pageref on input line 5847.
+\Hy@abspage=\count110
+\c@Item=\count111
+\c@Hfootnote=\count112
+)
+
+Package hyperref Message: Driver (autodetected): hpdftex.
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
+File: hpdftex.def 2012/05/13 v6.82q Hyperref driver for pdfTeX
+\Fld@listcount=\count113
+\c@bookmark@seq@number=\count114
+
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
+Package: rerunfilecheck 2011/04/15 v1.7 Rerun checks for auxiliary files (HO)
+Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
+82.
+)
+\Hy@SectionHShift=\skip48
+)
+(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
+Package: inputenc 2008/03/30 v1.1d Input encoding file
+\inpenc@prehook=\toks21
+\inpenc@posthook=\toks22
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
+File: utf8.def 2008/04/05 v1.1m UTF-8 support for inputenc
+Now handling font encoding OML ...
+... no UTF-8 mapping file for font encoding OML
+Now handling font encoding T1 ...
+... processing UTF-8 mapping file for font encoding T1
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu
+File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A1 (decimal 161)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00AB (decimal 171)
+ defining Unicode char U+00BB (decimal 187)
+ defining Unicode char U+00BF (decimal 191)
+ defining Unicode char U+00C0 (decimal 192)
+ defining Unicode char U+00C1 (decimal 193)
+ defining Unicode char U+00C2 (decimal 194)
+ defining Unicode char U+00C3 (decimal 195)
+ defining Unicode char U+00C4 (decimal 196)
+ defining Unicode char U+00C5 (decimal 197)
+ defining Unicode char U+00C6 (decimal 198)
+ defining Unicode char U+00C7 (decimal 199)
+ defining Unicode char U+00C8 (decimal 200)
+ defining Unicode char U+00C9 (decimal 201)
+ defining Unicode char U+00CA (decimal 202)
+ defining Unicode char U+00CB (decimal 203)
+ defining Unicode char U+00CC (decimal 204)
+ defining Unicode char U+00CD (decimal 205)
+ defining Unicode char U+00CE (decimal 206)
+ defining Unicode char U+00CF (decimal 207)
+ defining Unicode char U+00D0 (decimal 208)
+ defining Unicode char U+00D1 (decimal 209)
+ defining Unicode char U+00D2 (decimal 210)
+ defining Unicode char U+00D3 (decimal 211)
+ defining Unicode char U+00D4 (decimal 212)
+ defining Unicode char U+00D5 (decimal 213)
+ defining Unicode char U+00D6 (decimal 214)
+ defining Unicode char U+00D8 (decimal 216)
+ defining Unicode char U+00D9 (decimal 217)
+ defining Unicode char U+00DA (decimal 218)
+ defining Unicode char U+00DB (decimal 219)
+ defining Unicode char U+00DC (decimal 220)
+ defining Unicode char U+00DD (decimal 221)
+ defining Unicode char U+00DE (decimal 222)
+ defining Unicode char U+00DF (decimal 223)
+ defining Unicode char U+00E0 (decimal 224)
+ defining Unicode char U+00E1 (decimal 225)
+ defining Unicode char U+00E2 (decimal 226)
+ defining Unicode char U+00E3 (decimal 227)
+ defining Unicode char U+00E4 (decimal 228)
+ defining Unicode char U+00E5 (decimal 229)
+ defining Unicode char U+00E6 (decimal 230)
+ defining Unicode char U+00E7 (decimal 231)
+ defining Unicode char U+00E8 (decimal 232)
+ defining Unicode char U+00E9 (decimal 233)
+ defining Unicode char U+00EA (decimal 234)
+ defining Unicode char U+00EB (decimal 235)
+ defining Unicode char U+00EC (decimal 236)
+ defining Unicode char U+00ED (decimal 237)
+ defining Unicode char U+00EE (decimal 238)
+ defining Unicode char U+00EF (decimal 239)
+ defining Unicode char U+00F0 (decimal 240)
+ defining Unicode char U+00F1 (decimal 241)
+ defining Unicode char U+00F2 (decimal 242)
+ defining Unicode char U+00F3 (decimal 243)
+ defining Unicode char U+00F4 (decimal 244)
+ defining Unicode char U+00F5 (decimal 245)
+ defining Unicode char U+00F6 (decimal 246)
+ defining Unicode char U+00F8 (decimal 248)
+ defining Unicode char U+00F9 (decimal 249)
+ defining Unicode char U+00FA (decimal 250)
+ defining Unicode char U+00FB (decimal 251)
+ defining Unicode char U+00FC (decimal 252)
+ defining Unicode char U+00FD (decimal 253)
+ defining Unicode char U+00FE (decimal 254)
+ defining Unicode char U+00FF (decimal 255)
+ defining Unicode char U+0102 (decimal 258)
+ defining Unicode char U+0103 (decimal 259)
+ defining Unicode char U+0104 (decimal 260)
+ defining Unicode char U+0105 (decimal 261)
+ defining Unicode char U+0106 (decimal 262)
+ defining Unicode char U+0107 (decimal 263)
+ defining Unicode char U+010C (decimal 268)
+ defining Unicode char U+010D (decimal 269)
+ defining Unicode char U+010E (decimal 270)
+ defining Unicode char U+010F (decimal 271)
+ defining Unicode char U+0110 (decimal 272)
+ defining Unicode char U+0111 (decimal 273)
+ defining Unicode char U+0118 (decimal 280)
+ defining Unicode char U+0119 (decimal 281)
+ defining Unicode char U+011A (decimal 282)
+ defining Unicode char U+011B (decimal 283)
+ defining Unicode char U+011E (decimal 286)
+ defining Unicode char U+011F (decimal 287)
+ defining Unicode char U+0130 (decimal 304)
+ defining Unicode char U+0131 (decimal 305)
+ defining Unicode char U+0132 (decimal 306)
+ defining Unicode char U+0133 (decimal 307)
+ defining Unicode char U+0139 (decimal 313)
+ defining Unicode char U+013A (decimal 314)
+ defining Unicode char U+013D (decimal 317)
+ defining Unicode char U+013E (decimal 318)
+ defining Unicode char U+0141 (decimal 321)
+ defining Unicode char U+0142 (decimal 322)
+ defining Unicode char U+0143 (decimal 323)
+ defining Unicode char U+0144 (decimal 324)
+ defining Unicode char U+0147 (decimal 327)
+ defining Unicode char U+0148 (decimal 328)
+ defining Unicode char U+014A (decimal 330)
+ defining Unicode char U+014B (decimal 331)
+ defining Unicode char U+0150 (decimal 336)
+ defining Unicode char U+0151 (decimal 337)
+ defining Unicode char U+0152 (decimal 338)
+ defining Unicode char U+0153 (decimal 339)
+ defining Unicode char U+0154 (decimal 340)
+ defining Unicode char U+0155 (decimal 341)
+ defining Unicode char U+0158 (decimal 344)
+ defining Unicode char U+0159 (decimal 345)
+ defining Unicode char U+015A (decimal 346)
+ defining Unicode char U+015B (decimal 347)
+ defining Unicode char U+015E (decimal 350)
+ defining Unicode char U+015F (decimal 351)
+ defining Unicode char U+0160 (decimal 352)
+ defining Unicode char U+0161 (decimal 353)
+ defining Unicode char U+0162 (decimal 354)
+ defining Unicode char U+0163 (decimal 355)
+ defining Unicode char U+0164 (decimal 356)
+ defining Unicode char U+0165 (decimal 357)
+ defining Unicode char U+016E (decimal 366)
+ defining Unicode char U+016F (decimal 367)
+ defining Unicode char U+0170 (decimal 368)
+ defining Unicode char U+0171 (decimal 369)
+ defining Unicode char U+0178 (decimal 376)
+ defining Unicode char U+0179 (decimal 377)
+ defining Unicode char U+017A (decimal 378)
+ defining Unicode char U+017B (decimal 379)
+ defining Unicode char U+017C (decimal 380)
+ defining Unicode char U+017D (decimal 381)
+ defining Unicode char U+017E (decimal 382)
+ defining Unicode char U+200C (decimal 8204)
+ defining Unicode char U+2013 (decimal 8211)
+ defining Unicode char U+2014 (decimal 8212)
+ defining Unicode char U+2018 (decimal 8216)
+ defining Unicode char U+2019 (decimal 8217)
+ defining Unicode char U+201A (decimal 8218)
+ defining Unicode char U+201C (decimal 8220)
+ defining Unicode char U+201D (decimal 8221)
+ defining Unicode char U+201E (decimal 8222)
+ defining Unicode char U+2030 (decimal 8240)
+ defining Unicode char U+2031 (decimal 8241)
+ defining Unicode char U+2039 (decimal 8249)
+ defining Unicode char U+203A (decimal 8250)
+ defining Unicode char U+2423 (decimal 9251)
+)
+Now handling font encoding OT1 ...
+... processing UTF-8 mapping file for font encoding OT1
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu
+File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A1 (decimal 161)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00B8 (decimal 184)
+ defining Unicode char U+00BF (decimal 191)
+ defining Unicode char U+00C5 (decimal 197)
+ defining Unicode char U+00C6 (decimal 198)
+ defining Unicode char U+00D8 (decimal 216)
+ defining Unicode char U+00DF (decimal 223)
+ defining Unicode char U+00E6 (decimal 230)
+ defining Unicode char U+00EC (decimal 236)
+ defining Unicode char U+00ED (decimal 237)
+ defining Unicode char U+00EE (decimal 238)
+ defining Unicode char U+00EF (decimal 239)
+ defining Unicode char U+00F8 (decimal 248)
+ defining Unicode char U+0131 (decimal 305)
+ defining Unicode char U+0141 (decimal 321)
+ defining Unicode char U+0142 (decimal 322)
+ defining Unicode char U+0152 (decimal 338)
+ defining Unicode char U+0153 (decimal 339)
+ defining Unicode char U+2013 (decimal 8211)
+ defining Unicode char U+2014 (decimal 8212)
+ defining Unicode char U+2018 (decimal 8216)
+ defining Unicode char U+2019 (decimal 8217)
+ defining Unicode char U+201C (decimal 8220)
+ defining Unicode char U+201D (decimal 8221)
+)
+Now handling font encoding OMS ...
+... processing UTF-8 mapping file for font encoding OMS
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu
+File: omsenc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A7 (decimal 167)
+ defining Unicode char U+00B6 (decimal 182)
+ defining Unicode char U+00B7 (decimal 183)
+ defining Unicode char U+2020 (decimal 8224)
+ defining Unicode char U+2021 (decimal 8225)
+ defining Unicode char U+2022 (decimal 8226)
+)
+Now handling font encoding OMX ...
+... no UTF-8 mapping file for font encoding OMX
+Now handling font encoding U ...
+... no UTF-8 mapping file for font encoding U
+Now handling font encoding PD1 ...
+... no UTF-8 mapping file for font encoding PD1
+ defining Unicode char U+00A9 (decimal 169)
+ defining Unicode char U+00AA (decimal 170)
+ defining Unicode char U+00AE (decimal 174)
+ defining Unicode char U+00BA (decimal 186)
+ defining Unicode char U+02C6 (decimal 710)
+ defining Unicode char U+02DC (decimal 732)
+ defining Unicode char U+200C (decimal 8204)
+ defining Unicode char U+2026 (decimal 8230)
+ defining Unicode char U+2122 (decimal 8482)
+ defining Unicode char U+2423 (decimal 9251)
+))
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+))
+(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
+Package: ae 2001/02/12 1.3 Almost European Computer Modern
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
+File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
+LaTeX Font Info: Redeclaring font encoding T1 on input line 43.
+)
+LaTeX Font Info: Try loading font information for T1+aer on input line 100.
+
+(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd
+File: t1aer.fd 1997/11/16 Font definitions for T1/aer.
+)))
+(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
+Package: fancyvrb 2008/02/07
+
+Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
+<2008/02/07> (tvz)
+\FV@CodeLineNo=\count115
+\FV@InFile=\read1
+\FV@TabBox=\box28
+\c@FancyVerbLine=\count116
+\FV@StepNumber=\count117
+\FV@OutFile=\write3
+) (/usr/share/texmf/tex/latex/R/tex/latex/upquote.sty
+Package: upquote 2003/08/11 v1.1 Covington's upright-quote modification to verb
+atim and verb
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
+Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
+Package textcomp Info: Sub-encoding information:
+(textcomp) 5 = only ISO-Adobe without \textcurrency
+(textcomp) 4 = 5 + \texteuro
+(textcomp) 3 = 4 + \textohm
+(textcomp) 2 = 3 + \textestimated + \textcurrency
+(textcomp) 1 = TS1 - \textcircled - \t
+(textcomp) 0 = TS1 (full)
+(textcomp) Font families with sub-encoding setting implement
+(textcomp) only a restricted character set as indicated.
+(textcomp) Family '?' is the default used for unknown fonts.
+(textcomp) See the documentation for details.
+Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
+File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
+Now handling font encoding TS1 ...
+... processing UTF-8 mapping file for font encoding TS1
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu
+File: ts1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc
+ defining Unicode char U+00A2 (decimal 162)
+ defining Unicode char U+00A3 (decimal 163)
+ defining Unicode char U+00A4 (decimal 164)
+ defining Unicode char U+00A5 (decimal 165)
+ defining Unicode char U+00A6 (decimal 166)
+ defining Unicode char U+00A7 (decimal 167)
+ defining Unicode char U+00A8 (decimal 168)
+ defining Unicode char U+00A9 (decimal 169)
+ defining Unicode char U+00AA (decimal 170)
+ defining Unicode char U+00AC (decimal 172)
+ defining Unicode char U+00AE (decimal 174)
+ defining Unicode char U+00AF (decimal 175)
+ defining Unicode char U+00B0 (decimal 176)
+ defining Unicode char U+00B1 (decimal 177)
+ defining Unicode char U+00B2 (decimal 178)
+ defining Unicode char U+00B3 (decimal 179)
+ defining Unicode char U+00B4 (decimal 180)
+ defining Unicode char U+00B5 (decimal 181)
+ defining Unicode char U+00B6 (decimal 182)
+ defining Unicode char U+00B7 (decimal 183)
+ defining Unicode char U+00B9 (decimal 185)
+ defining Unicode char U+00BA (decimal 186)
+ defining Unicode char U+00BC (decimal 188)
+ defining Unicode char U+00BD (decimal 189)
+ defining Unicode char U+00BE (decimal 190)
+ defining Unicode char U+00D7 (decimal 215)
+ defining Unicode char U+00F7 (decimal 247)
+ defining Unicode char U+0192 (decimal 402)
+ defining Unicode char U+02C7 (decimal 711)
+ defining Unicode char U+02D8 (decimal 728)
+ defining Unicode char U+02DD (decimal 733)
+ defining Unicode char U+0E3F (decimal 3647)
+ defining Unicode char U+2016 (decimal 8214)
+ defining Unicode char U+2020 (decimal 8224)
+ defining Unicode char U+2021 (decimal 8225)
+ defining Unicode char U+2022 (decimal 8226)
+ defining Unicode char U+2030 (decimal 8240)
+ defining Unicode char U+2031 (decimal 8241)
+ defining Unicode char U+203B (decimal 8251)
+ defining Unicode char U+203D (decimal 8253)
+ defining Unicode char U+2044 (decimal 8260)
+ defining Unicode char U+204E (decimal 8270)
+ defining Unicode char U+2052 (decimal 8274)
+ defining Unicode char U+20A1 (decimal 8353)
+ defining Unicode char U+20A4 (decimal 8356)
+ defining Unicode char U+20A6 (decimal 8358)
+ defining Unicode char U+20A9 (decimal 8361)
+ defining Unicode char U+20AB (decimal 8363)
+ defining Unicode char U+20AC (decimal 8364)
+ defining Unicode char U+20B1 (decimal 8369)
+ defining Unicode char U+2103 (decimal 8451)
+ defining Unicode char U+2116 (decimal 8470)
+ defining Unicode char U+2117 (decimal 8471)
+ defining Unicode char U+211E (decimal 8478)
+ defining Unicode char U+2120 (decimal 8480)
+ defining Unicode char U+2122 (decimal 8482)
+ defining Unicode char U+2126 (decimal 8486)
+ defining Unicode char U+2127 (decimal 8487)
+ defining Unicode char U+212E (decimal 8494)
+ defining Unicode char U+2190 (decimal 8592)
+ defining Unicode char U+2191 (decimal 8593)
+ defining Unicode char U+2192 (decimal 8594)
+ defining Unicode char U+2193 (decimal 8595)
+ defining Unicode char U+2329 (decimal 9001)
+ defining Unicode char U+232A (decimal 9002)
+ defining Unicode char U+2422 (decimal 9250)
+ defining Unicode char U+25E6 (decimal 9702)
+ defining Unicode char U+25EF (decimal 9711)
+ defining Unicode char U+266A (decimal 9834)
+))
+LaTeX Info: Redefining \oldstylenums on input line 266.
+Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
+Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
+Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
+Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
+Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
+Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
+Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
+Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
+Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
+Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
+Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
+Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
+Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
+Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
+Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
+Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
+Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
+Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
+Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
+Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
+Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
+Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
+Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
+Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
+
+Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
+Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
+Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
+Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
+Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
+Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
+Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 311.
+Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 312.
+Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 313.
+Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 314.
+Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 315.
+Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 316.
+Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 317.
+Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 318.
+Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 319.
+Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 320.
+Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 321.
+Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 322.
+Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 323.
+Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 324.
+Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 325.
+Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 326.
+Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 327.
+Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 328.
+Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 329.
+Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 330.
+Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 331.
+Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 332.
+Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 333.
+Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 334.
+Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 335.
+Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 336.
+Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 337.
+Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 338.
+Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 339.
+Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 340.
+))
+(/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty
+Package: relsize 2011/09/21 ver 4.0
+
+Examine \normalsize starts \@setfontsize size may be \@xiipt.
+Examine \small starts \@setfontsize size may be \@xipt.
+Examine \footnotesize starts \@setfontsize size may be \@xpt.
+Examine \large starts \@setfontsize size may be \@xivpt.
+Examine \Large starts \@setfontsize size may be \@xviipt.
+Examine \LARGE starts \@setfontsize size may be \@xxpt.
+Examine \scriptsize starts \@setfontsize size may be \@viiipt.
+Examine \tiny starts \@setfontsize size may be \@vipt.
+Examine \huge starts \@setfontsize size may be \@xxvpt.
+Examine \Huge starts \@setfontsize size may be \@xxvpt. ))
+Package hyperref Info: Option `colorlinks' set `true' on input line 19.
+
+
+Package hyperref Warning: Option `hyperindex' has already been used,
+(hyperref) setting the option has no effect on input line 19.
+
+Package hyperref Info: Option `linktocpage' set `true' on input line 19.
+(./examples.aux)
+\openout1 = `examples.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 21.
+LaTeX Font Info: ... okay on input line 21.
+LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 21.
+LaTeX Font Info: Try loading font information for TS1+cmr on input line 21.
+ (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd
+File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
+)
+LaTeX Font Info: ... okay on input line 21.
+
+(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
+[Loading MPS to PDF converter (version 2006.09.02).]
+\scratchcounter=\count118
+\scratchdimen=\dimen130
+\scratchbox=\box29
+\nofMPsegments=\count119
+\nofMParguments=\count120
+\everyMPshowfont=\toks23
+\MPscratchCnt=\count121
+\MPscratchDim=\dimen131
+\MPnumerator=\count122
+\makeMPintoPDFobject=\count123
+\everyMPtoPDFconversion=\toks24
+) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
+Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf
+
+(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
+Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)
+)
+Package grfext Info: Graphics extension search list:
+(grfext) [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE
+G,.JBIG2,.JB2,.eps]
+(grfext) \AppendGraphicsExtensions on input line 452.
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
+File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
+e
+))
+\AtBeginShipoutBox=\box30
+
+(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
+Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC)
+
+(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg
+File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
+)
+Package color Info: Driver file: pdftex.def on input line 130.
+)
+Package hyperref Info: Link coloring ON on input line 21.
+
+(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
+Package: nameref 2010/04/30 v2.40 Cross-referencing by name of section
+
+(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty
+Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO)
+)
+\c@section@level=\count124
+)
+LaTeX Info: Redefining \ref on input line 21.
+LaTeX Info: Redefining \pageref on input line 21.
+LaTeX Info: Redefining \nameref on input line 21.
+
+(./examples.out) (./examples.out)
+\@outlinefile=\write4
+\openout4 = `examples.out'.
+
+LaTeX Font Info: Try loading font information for U+msa on input line 31.
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd
+File: umsa.fd 2009/06/22 v3.00 AMS symbols A
+)
+LaTeX Font Info: Try loading font information for U+msb on input line 31.
+
+(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd
+File: umsb.fd 2009/06/22 v3.00 AMS symbols B
+)
+LaTeX Font Info: Try loading font information for U+lasy on input line 31.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd
+File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions
+) [0
+
+{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./examples.toc)
+\tf@toc=\write5
+\openout5 = `examples.toc'.
+
+LaTeX Font Info: Try loading font information for T1+aett on input line 57.
+
+(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd
+File: t1aett.fd 1997/11/16 Font definitions for T1/aett.
+) [1
+
+]
+LaTeX Font Info: Try loading font information for T1+pcr on input line 94.
+
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd
+File: t1pcr.fd 2001/06/04 font definitions for T1/pcr.
+)
+LaTeX Font Info: Font shape `T1/pcr/m/it' in size <10> not available
+(Font) Font shape `T1/pcr/m/sl' tried instead on input line 94.
+ [2]
+<examples-L1_SFO_plot.pdf, id=58, 433.62pt x 433.62pt>
+File: examples-L1_SFO_plot.pdf Graphic file (type pdf)
+
+<use examples-L1_SFO_plot.pdf>
+Package pdftex.def Info: examples-L1_SFO_plot.pdf used on input line 171.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [3]
+<examples-L1_SFO_residuals.pdf, id=63, 433.62pt x 433.62pt>
+File: examples-L1_SFO_residuals.pdf Graphic file (type pdf)
+
+<use examples-L1_SFO_residuals.pdf>
+Package pdftex.def Info: examples-L1_SFO_residuals.pdf used on input line 184.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [4 <./examples-L1_SFO_plot.pdf>] [5 <./examples-L1_SFO_residuals.pdf>] [6]
+<examples-L2_SFO_plot.pdf, id=91, 433.62pt x 433.62pt>
+File: examples-L2_SFO_plot.pdf Graphic file (type pdf)
+
+<use examples-L2_SFO_plot.pdf>
+Package pdftex.def Info: examples-L2_SFO_plot.pdf used on input line 302.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [7]
+<examples-L2_SFO_residuals.pdf, id=96, 433.62pt x 433.62pt>
+File: examples-L2_SFO_residuals.pdf Graphic file (type pdf)
+
+<use examples-L2_SFO_residuals.pdf>
+Package pdftex.def Info: examples-L2_SFO_residuals.pdf used on input line 315.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [8 <./examples-L2_SFO_plot.pdf>]
+<examples-L2_FOMC.pdf, id=107, 433.62pt x 433.62pt>
+File: examples-L2_FOMC.pdf Graphic file (type pdf)
+ <use examples-L2_FOMC.pdf>
+Package pdftex.def Info: examples-L2_FOMC.pdf used on input line 337.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[9 <./examples-L2_SFO_residuals.pdf>]
+<examples-L2_DFOP.pdf, id=118, 433.62pt x 433.62pt>
+File: examples-L2_DFOP.pdf Graphic file (type pdf)
+ <use examples-L2_DFOP.pdf>
+Package pdftex.def Info: examples-L2_DFOP.pdf used on input line 352.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[10 <./examples-L2_FOMC.pdf>] [11 <./examples-L2_DFOP.pdf>] [12]
+<examples-L2_DFOP_2.pdf, id=144, 433.62pt x 433.62pt>
+File: examples-L2_DFOP_2.pdf Graphic file (type pdf)
+
+<use examples-L2_DFOP_2.pdf>
+Package pdftex.def Info: examples-L2_DFOP_2.pdf used on input line 439.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [13] [14 <./examples-L2_DFOP_2.pdf>] [15]
+<examples-L3_SFO.pdf, id=164, 433.62pt x 433.62pt>
+File: examples-L3_SFO.pdf Graphic file (type pdf)
+ <use examples-L3_SFO.pdf>
+Package pdftex.def Info: examples-L3_SFO.pdf used on input line 528.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[16] [17 <./examples-L3_SFO.pdf>]
+<examples-L3_FOMC.pdf, id=179, 433.62pt x 433.62pt>
+File: examples-L3_FOMC.pdf Graphic file (type pdf)
+ <use examples-L3_FOMC.pdf>
+Package pdftex.def Info: examples-L3_FOMC.pdf used on input line 562.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[18 <./examples-L3_FOMC.pdf>]
+<examples-L3_DFOP.pdf, id=191, 433.62pt x 433.62pt>
+File: examples-L3_DFOP.pdf Graphic file (type pdf)
+ <use examples-L3_DFOP.pdf>
+Package pdftex.def Info: examples-L3_DFOP.pdf used on input line 582.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[19 <./examples-L3_DFOP.pdf>] [20]
+<examples-L4_SFO.pdf, id=206, 433.62pt x 433.62pt>
+File: examples-L4_SFO.pdf Graphic file (type pdf)
+ <use examples-L4_SFO.pdf>
+Package pdftex.def Info: examples-L4_SFO.pdf used on input line 671.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+
+[21] <examples-L4_FOMC.pdf, id=211, 433.62pt x 433.62pt>
+File: examples-L4_FOMC.pdf Graphic file (type pdf)
+
+<use examples-L4_FOMC.pdf>
+Package pdftex.def Info: examples-L4_FOMC.pdf used on input line 691.
+(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
+ [22 <./examples-L4_SFO.pdf>] (./examples.bbl
+[23 <./examples-L4_FOMC.pdf>])
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 699.
+ [24]
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 699.
+ (./examples.aux)
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 699.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 699.
+Package rerunfilecheck Info: File `examples.out' has not changed.
+(rerunfilecheck) Checksum: 3F5170E33F755296C8437680AEA1EFF7;343.
+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 699.
+ )
+Here is how much of TeX's memory you used:
+ 7873 strings out of 495007
+ 111249 string characters out of 3179690
+ 187564 words of memory out of 3000000
+ 10839 multiletter control sequences out of 15000+200000
+ 38268 words of font info for 93 fonts, out of 3000000 for 9000
+ 14 hyphenation exceptions out of 8191
+ 31i,6n,28p,255b,512s stack positions out of 5000i,500n,10000p,200000b,50000s
+{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texliv
+e/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf
+-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/
+fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/
+type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
+ublic/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
+msfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
+cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmt
+t12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb>
+Output written on examples.pdf (25 pages, 184683 bytes).
+PDF statistics:
+ 283 PDF objects out of 1000 (max. 8388607)
+ 220 compressed objects within 3 object streams
+ 36 named destinations out of 1000 (max. 500000)
+ 101 words of extra memory for PDF output out of 10000 (max. 10000000)
+
diff --git a/vignettes/examples.out b/vignettes/examples.out
new file mode 100644
index 00000000..0ccdd62b
--- /dev/null
+++ b/vignettes/examples.out
@@ -0,0 +1,5 @@
+\BOOKMARK [1][-]{section.1}{Kinetic evaluations for parent compounds}{}% 1
+\BOOKMARK [2][-]{subsection.1.1}{Laboratory Data L1}{section.1}% 2
+\BOOKMARK [2][-]{subsection.1.2}{Laboratory Data L2}{section.1}% 3
+\BOOKMARK [2][-]{subsection.1.3}{Laboratory Data L3}{section.1}% 4
+\BOOKMARK [2][-]{subsection.1.4}{Laboratory Data L4}{section.1}% 5
diff --git a/vignettes/examples.pdf b/vignettes/examples.pdf
new file mode 100644
index 00000000..be0d96e5
--- /dev/null
+++ b/vignettes/examples.pdf
Binary files differ
diff --git a/vignettes/examples.tex b/vignettes/examples.tex
new file mode 100644
index 00000000..4f59aa24
--- /dev/null
+++ b/vignettes/examples.tex
@@ -0,0 +1,700 @@
+% $Id: examples.Rnw 66 2010-09-03 08:50:26Z jranke $
+%%\VignetteIndexEntry{Examples for kinetic evaluations using mkin}
+%%VignetteDepends{FME}
+%%\usepackage{Sweave}
+\documentclass[12pt,a4paper]{article}
+\usepackage{a4wide}
+%%\usepackage[lists,heads]{endfloat}
+\input{header}
+\hypersetup{
+ pdftitle = {Examples for kinetic evaluations using mkin},
+ pdfsubject = {Manuscript},
+ pdfauthor = {Johannes Ranke},
+ colorlinks = {true},
+ linkcolor = {blue},
+ citecolor = {blue},
+ urlcolor = {red},
+ hyperindex = {true},
+ linktocpage = {true},
+}
+
+\begin{document}
+\title{Examples for kinetic evaluations using mkin}
+\author{\textbf{Johannes Ranke} \\[0.5cm]
+%EndAName
+Eurofins Regulatory AG\\
+Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm]
+and\\[0.5cm]
+University of Bremen\\
+}
+\maketitle
+
+%\begin{abstract}
+%\end{abstract}
+
+
+\thispagestyle{empty} \setcounter{page}{0}
+
+\clearpage
+
+\tableofcontents
+
+\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
+
+\section{Kinetic evaluations for parent compounds}
+\label{intro}
+
+These examples are also evaluated in a parallel vignette of the
+\Rpackage{kinfit} package \citep{pkg:kinfit}. The datasets are from Appendix 3,
+of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}.
+
+\subsection{Laboratory Data L1}
+
+The following code defines example dataset L1 from the FOCUS kinetics
+report, p. 284
+
+\begin{Schunk}
+\begin{Sinput}
+R> library("mkin")
+R> FOCUS_2006_L1 = data.frame(
++ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
++ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
++ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
++ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
+R> FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
+\end{Sinput}
+\end{Schunk}
+
+The next step is to set up the models used for the kinetic analysis. Note that
+the model definitions contain the names of the observed variables in the data.
+In this case, there is only one variable called \Robject{parent}.
+
+\begin{Schunk}
+\begin{Sinput}
+R> SFO <- mkinmod(parent = list(type = "SFO"))
+R> FOMC <- mkinmod(parent = list(type = "FOMC"))
+R> DFOP <- mkinmod(parent = list(type = "DFOP"))
+\end{Sinput}
+\end{Schunk}
+
+The three models cover the first assumption of simple first order (SFO),
+the case of declining rate constant over time (FOMC) and the case of two
+different phases of the kinetics (DFOP). For a more detailed discussion
+of the models, please see the FOCUS kinetics report.
+
+The following two lines fit the model and produce the summary report
+of the model fit. This covers the numerical analysis given in the
+FOCUS report.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
+R> summary(m.L1.SFO)
+\end{Sinput}
+\begin{Soutput}
+mkin version: 0.9.10
+R version: 2.15.2
+Date of fit: Sat Feb 16 21:38:15 2013
+Date of summary: Sat Feb 16 21:38:15 2013
+
+Equations:
+[1] d_parent = - k_parent_sink * parent
+
+Starting values for optimised parameters:
+ initial type transformed
+parent_0 100.0 state 100.000000
+k_parent_sink 0.1 deparm -2.302585
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters:
+ Estimate Std. Error
+parent_0 92.471 1.368
+k_parent_sink -2.347 0.041
+
+Backtransformed parameters:
+ Estimate
+parent_0 92.471
+k_parent_sink 0.096
+
+Residual standard error: 2.948 on 16 degrees of freedom
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 3.424 2 7
+parent 3.424 2 7
+
+Estimated disappearance times:
+ DT50 DT90
+parent 7.249 24.08
+
+Estimated formation fractions:
+ ff
+parent_sink 1
+
+Parameter correlation:
+ parent_0 k_parent_sink
+parent_0 1.0000 0.6248
+k_parent_sink 0.6248 1.0000
+
+Data:
+ time variable observed predicted residual
+ 0 parent 88.3 92.471 -4.1710
+ 0 parent 91.4 92.471 -1.0710
+ 1 parent 85.6 84.039 1.5610
+ 1 parent 84.5 84.039 0.4610
+ 2 parent 78.9 76.376 2.5241
+ 2 parent 77.6 76.376 1.2241
+ 3 parent 72.0 69.412 2.5884
+ 3 parent 71.9 69.412 2.4884
+ 5 parent 50.3 57.330 -7.0301
+ 5 parent 59.4 57.330 2.0699
+ 7 parent 47.0 47.352 -0.3515
+ 7 parent 45.1 47.352 -2.2515
+ 14 parent 27.7 24.247 3.4527
+ 14 parent 27.3 24.247 3.0527
+ 21 parent 10.0 12.416 -2.4163
+ 21 parent 10.4 12.416 -2.0163
+ 30 parent 2.9 5.251 -2.3513
+ 30 parent 4.0 5.251 -1.2513
+\end{Soutput}
+\end{Schunk}
+
+A plot of the fit is obtained with the plot function for mkinfit objects.
+
+\begin{Schunk}
+\begin{Sinput}
+R> plot(m.L1.SFO)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L1_SFO_plot}
+
+The residual plot can be obtained using the information contained in the
+mkinfit object, which is in fact a derivative of an modFit object defined by
+the \Rpackage{FME} package.
+
+\begin{Schunk}
+\begin{Sinput}
+R> plot(m.L1.SFO$data$time, m.L1.SFO$data$residual,
++ xlab = "Time", ylab = "Residual", ylim = c(-8, 8))
+R> abline(h = 0, lty = 2)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L1_SFO_residuals}
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
+R> s.m.L1.FOMC <- summary(m.L1.FOMC)
+R> s.m.L1.FOMC$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.03618911 3 6
+parent 0.03618911 3 6
+\end{Soutput}
+\end{Schunk}
+
+Due to the higher number of parameters, and the lower number of degrees of freedom
+of the fit, the $\chi^2$ error level is actually higher for the FOMC model (3.6\%) than
+for the SFO model (3.4\%).
+
+\subsection{Laboratory Data L2}
+
+The following code defines example dataset L2 from the FOCUS kinetics
+report, p. 287
+
+\begin{Schunk}
+\begin{Sinput}
+R> library("mkin")
+R> FOCUS_2006_L2 = data.frame(
++ t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
++ parent = c(96.1, 91.8, 41.4, 38.7,
++ 19.3, 22.3, 4.6, 4.6,
++ 2.6, 1.2, 0.3, 0.6))
+R> FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
+\end{Sinput}
+\end{Schunk}
+
+Again, the SFO model is fitted and a summary is obtained.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
+R> summary(m.L2.SFO)
+\end{Sinput}
+\begin{Soutput}
+mkin version: 0.9.10
+R version: 2.15.2
+Date of fit: Sat Feb 16 21:38:15 2013
+Date of summary: Sat Feb 16 21:38:15 2013
+
+Equations:
+[1] d_parent = - k_parent_sink * parent
+
+Starting values for optimised parameters:
+ initial type transformed
+parent_0 100.0 state 100.000000
+k_parent_sink 0.1 deparm -2.302585
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters:
+ Estimate Std. Error
+parent_0 91.4656 3.807
+k_parent_sink -0.4112 0.107
+
+Backtransformed parameters:
+ Estimate
+parent_0 91.466
+k_parent_sink 0.663
+
+Residual standard error: 5.51 on 10 degrees of freedom
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 14.38 2 4
+parent 14.38 2 4
+
+Estimated disappearance times:
+ DT50 DT90
+parent 1.046 3.474
+
+Estimated formation fractions:
+ ff
+parent_sink 1
+
+Parameter correlation:
+ parent_0 k_parent_sink
+parent_0 1.0000 0.4295
+k_parent_sink 0.4295 1.0000
+
+Data:
+ time variable observed predicted residual
+ 0 parent 96.1 91.4656079103 4.6344
+ 0 parent 91.8 91.4656079103 0.3344
+ 1 parent 41.4 47.1395280371 -5.7395
+ 1 parent 38.7 47.1395280371 -8.4395
+ 3 parent 19.3 12.5210295280 6.7790
+ 3 parent 22.3 12.5210295280 9.7790
+ 7 parent 4.6 0.8833842647 3.7166
+ 7 parent 4.6 0.8833842647 3.7166
+ 14 parent 2.6 0.0085318162 2.5915
+ 14 parent 1.2 0.0085318162 1.1915
+ 28 parent 0.3 0.0000007958 0.3000
+ 28 parent 0.6 0.0000007958 0.6000
+\end{Soutput}
+\end{Schunk}
+
+The $\chi^2$ error level of 14\% suggests that the model does not fit very well.
+This is also obvious from the plots of the fit and the residuals.
+
+\begin{Schunk}
+\begin{Sinput}
+R> plot(m.L2.SFO)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L2_SFO_plot}
+
+In the FOCUS kinetics report, it is stated that there is no apparent systematic
+error observed from the residual plot up to the measured DT90 (approximately at
+day 5), and there is an underestimation beyond that point.
+
+\begin{Schunk}
+\begin{Sinput}
+R> plot(m.L2.SFO$data$time, m.L2.SFO$data$residual,
++ xlab = "Time", ylab = "Residual", ylim = c(-10, 10))
+R> abline(h = 0, lty = 2)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L2_SFO_residuals}
+
+We may add that it is difficult to judge the random nature of the residuals just
+from the three samplings at days 0, 1 and 3. Also, it is not clear why a
+consistent underestimation after the approximate DT90 should be irrelevant.
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet=TRUE)
+R> plot(m.L2.FOMC)
+R> s.m.L2.FOMC <- summary(m.L2.FOMC)
+R> s.m.L2.FOMC$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.06204245 3 3
+parent 0.06204245 3 3
+\end{Soutput}
+\end{Schunk}
+\includegraphics{examples-L2_FOMC}
+
+The error level at which the $\chi^2$ test passes is much lower in this case.
+Therefore, the FOMC model provides a better description of the data, as less
+experimental error has to be assumed in order to explain the data.
+
+Fitting the four parameter DFOP model does not further reduce the
+$\chi^2$ error level.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet=TRUE)
+R> plot(m.L2.DFOP)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L2_DFOP}
+
+Here, the default starting parameters for the DFOP model obviously do not lead
+to a reasonable solution. Therefore the fit is repeated with different starting
+parameters.
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
++ parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
++ quiet=TRUE)
+R> plot(m.L2.DFOP)
+R> summary(m.L2.DFOP)
+\end{Sinput}
+\begin{Soutput}
+mkin version: 0.9.10
+R version: 2.15.2
+Date of fit: Sat Feb 16 21:38:16 2013
+Date of summary: Sat Feb 16 21:38:16 2013
+
+Equations:
+[1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
+
+Starting values for optimised parameters:
+ initial type transformed
+parent_0 1e+02 state 100.0000000
+k1 1e+00 deparm 0.0000000
+k2 1e-02 deparm -4.6051702
+g 8e-01 deparm 0.9802581
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters:
+ Estimate Std. Error
+parent_0 93.9500 NA
+k1 4.9589 NA
+k2 -1.0880 NA
+g -0.2821 NA
+
+Backtransformed parameters:
+ Estimate
+parent_0 93.950
+k1 142.434
+k2 0.337
+g 0.402
+
+Residual standard error: 1.732 on 8 degrees of freedom
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 2.529 4 2
+parent 2.529 4 2
+
+Estimated disappearance times:
+ DT50 DT90
+parent NA NA
+
+Estimated formation fractions:
+[1] ff
+<0 rows> (or 0-length row.names)
+
+Data:
+ time variable observed predicted residual
+ 0 parent 96.1 93.950000 2.1500
+ 0 parent 91.8 93.950000 -2.1500
+ 1 parent 41.4 40.143423 1.2566
+ 1 parent 38.7 40.143423 -1.4434
+ 3 parent 19.3 20.464500 -1.1645
+ 3 parent 22.3 20.464500 1.8355
+ 7 parent 4.6 5.318322 -0.7183
+ 7 parent 4.6 5.318322 -0.7183
+ 14 parent 2.6 0.503070 2.0969
+ 14 parent 1.2 0.503070 0.6969
+ 28 parent 0.3 0.004501 0.2955
+ 28 parent 0.6 0.004501 0.5955
+\end{Soutput}
+\begin{Sinput}
+R> s.m.L2.DFOP <- summary(m.L2.DFOP)
+R> s.m.L2.DFOP$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.02528763 4 2
+parent 0.02528763 4 2
+\end{Soutput}
+\end{Schunk}
+\includegraphics{examples-L2_DFOP_2}
+
+Therefore, the FOMC model is clearly the best-fit model based on the
+$\chi^2$ error level criterion.
+
+\subsection{Laboratory Data L3}
+
+The following code defines example dataset L3 from the FOCUS kinetics
+report, p. 290
+
+\begin{Schunk}
+\begin{Sinput}
+R> library("mkin")
+R> FOCUS_2006_L3 = data.frame(
++ t = c(0, 3, 7, 14, 30, 60, 91, 120),
++ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
+R> FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
+\end{Sinput}
+\end{Schunk}
+
+SFO model, summary and plot:
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet=TRUE)
+R> summary(m.L3.SFO)
+\end{Sinput}
+\begin{Soutput}
+mkin version: 0.9.10
+R version: 2.15.2
+Date of fit: Sat Feb 16 21:38:16 2013
+Date of summary: Sat Feb 16 21:38:16 2013
+
+Equations:
+[1] d_parent = - k_parent_sink * parent
+
+Starting values for optimised parameters:
+ initial type transformed
+parent_0 100.0 state 100.000000
+k_parent_sink 0.1 deparm -2.302585
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters:
+ Estimate Std. Error
+parent_0 74.873 8.458
+k_parent_sink -3.678 0.326
+
+Backtransformed parameters:
+ Estimate
+parent_0 74.873
+k_parent_sink 0.025
+
+Residual standard error: 12.91 on 6 degrees of freedom
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 21.24 2 6
+parent 21.24 2 6
+
+Estimated disappearance times:
+ DT50 DT90
+parent 27.43 91.12
+
+Estimated formation fractions:
+ ff
+parent_sink 1
+
+Parameter correlation:
+ parent_0 k_parent_sink
+parent_0 1.0000 0.5484
+k_parent_sink 0.5484 1.0000
+
+Data:
+ time variable observed predicted residual
+ 0 parent 97.8 74.873 22.92734
+ 3 parent 60.0 69.407 -9.40654
+ 7 parent 51.0 62.734 -11.73403
+ 14 parent 43.0 52.563 -9.56336
+ 30 parent 35.0 35.083 -0.08281
+ 60 parent 22.0 16.439 5.56137
+ 91 parent 15.0 7.510 7.48961
+ 120 parent 12.0 3.609 8.39083
+\end{Soutput}
+\begin{Sinput}
+R> plot(m.L3.SFO)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L3_SFO}
+
+The $\chi^2$ error level of 22\% as well as the plot suggest that the model
+does not fit very well.
+
+The FOMC model performs better:
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet=TRUE)
+R> plot(m.L3.FOMC)
+R> s.m.L3.FOMC <- summary(m.L3.FOMC)
+R> s.m.L3.FOMC$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.07321867 3 5
+parent 0.07321867 3 5
+\end{Soutput}
+\begin{Sinput}
+R> endpoints(m.L3.FOMC)
+\end{Sinput}
+\begin{Soutput}
+$distimes
+ DT50 DT90
+parent 7.729478 431.2428
+
+$ff
+logical(0)
+
+$SFORB
+logical(0)
+\end{Soutput}
+\end{Schunk}
+\includegraphics{examples-L3_FOMC}
+
+The error level at which the $\chi^2$ test passes is 7\% in this case.
+
+Fitting the four parameter DFOP model further reduces the $\chi^2$ error level
+considerably:
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet=TRUE)
+R> plot(m.L3.DFOP)
+R> s.m.L3.DFOP <- summary(m.L3.DFOP)
+R> s.m.L3.DFOP$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.02223992 4 4
+parent 0.02223992 4 4
+\end{Soutput}
+\end{Schunk}
+\includegraphics{examples-L3_DFOP}
+
+Therefore, the DFOP model is the best-fit model based on the $\chi^2$ error
+level criterion for laboratory data L3.
+
+\subsection{Laboratory Data L4}
+
+The following code defines example dataset L4 from the FOCUS kinetics
+report, p. 293
+
+\begin{Schunk}
+\begin{Sinput}
+R> library("mkin")
+R> FOCUS_2006_L4 = data.frame(
++ t = c(0, 3, 7, 14, 30, 60, 91, 120),
++ parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
+R> FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
+\end{Sinput}
+\end{Schunk}
+
+SFO model, summary and plot:
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet=TRUE)
+R> summary(m.L4.SFO)
+\end{Sinput}
+\begin{Soutput}
+mkin version: 0.9.10
+R version: 2.15.2
+Date of fit: Sat Feb 16 21:38:17 2013
+Date of summary: Sat Feb 16 21:38:17 2013
+
+Equations:
+[1] d_parent = - k_parent_sink * parent
+
+Starting values for optimised parameters:
+ initial type transformed
+parent_0 100.0 state 100.000000
+k_parent_sink 0.1 deparm -2.302585
+
+Fixed parameter values:
+None
+
+Optimised, transformed parameters:
+ Estimate Std. Error
+parent_0 96.44 1.949
+k_parent_sink -5.03 0.080
+
+Backtransformed parameters:
+ Estimate
+parent_0 96.442
+k_parent_sink 0.007
+
+Residual standard error: 3.651 on 6 degrees of freedom
+
+Chi2 error levels in percent:
+ err.min n.optim df
+All data 3.288 2 6
+parent 3.288 2 6
+
+Estimated disappearance times:
+ DT50 DT90
+parent 106 352
+
+Estimated formation fractions:
+ ff
+parent_sink 1
+
+Parameter correlation:
+ parent_0 k_parent_sink
+parent_0 1.0000 0.5865
+k_parent_sink 0.5865 1.0000
+
+Data:
+ time variable observed predicted residual
+ 0 parent 96.6 96.44 0.1585
+ 3 parent 96.3 94.57 1.7324
+ 7 parent 94.3 92.13 2.1744
+ 14 parent 88.8 88.00 0.7972
+ 30 parent 74.9 79.26 -4.3589
+ 60 parent 59.9 65.14 -5.2376
+ 91 parent 53.5 53.18 0.3167
+ 120 parent 49.0 43.99 5.0054
+\end{Soutput}
+\begin{Sinput}
+R> plot(m.L4.SFO)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{examples-L4_SFO}
+
+The $\chi^2$ error level of 3.3\% as well as the plot suggest that the model
+fits very well.
+
+The FOMC model for comparison
+
+\begin{Schunk}
+\begin{Sinput}
+R> m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet=TRUE)
+R> plot(m.L4.FOMC)
+R> s.m.L4.FOMC <- summary(m.L4.FOMC)
+R> s.m.L4.FOMC$errmin
+\end{Sinput}
+\begin{Soutput}
+ err.min n.optim df
+All data 0.02027643 3 5
+parent 0.02027643 3 5
+\end{Soutput}
+\end{Schunk}
+\includegraphics{examples-L4_FOMC}
+
+The error level at which the $\chi^2$ test passes is slightly lower for the FOMC
+model. However, the difference appears negligible.
+
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+\end{document}
+% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.toc b/vignettes/examples.toc
new file mode 100644
index 00000000..f25aa62f
--- /dev/null
+++ b/vignettes/examples.toc
@@ -0,0 +1,5 @@
+\contentsline {section}{\numberline {1}Kinetic evaluations for parent compounds}{1}{section.1}
+\contentsline {subsection}{\numberline {1.1}Laboratory Data L1}{1}{subsection.1.1}
+\contentsline {subsection}{\numberline {1.2}Laboratory Data L2}{6}{subsection.1.2}
+\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{14}{subsection.1.3}
+\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{20}{subsection.1.4}

Contact - Imprint