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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-17 23:38:48 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2013-02-17 23:38:48 +0000
commitf92a65cd0d721731aea59847722fc69da1ab7ee5 (patch)
tree89dc8cc655715483f78e0c06944c1d53360ba3d8 /vignettes
parent3715219923dca43dcc6f317f92099d512b0c4a64 (diff)
- Removed vignette files that are built during generation
- Updated the staticdoc documentation git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@63 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/examples-FOCUS_2006_L3_2.pdfbin6609 -> 0 bytes
-rw-r--r--vignettes/examples-FOCUS_2006_L4.pdfbin6557 -> 0 bytes
-rw-r--r--vignettes/examples-L1_SFO_plot.pdfbin5572 -> 0 bytes
-rw-r--r--vignettes/examples-L1_SFO_residuals.pdfbin4718 -> 0 bytes
-rw-r--r--vignettes/examples-L2_plot.pdfbin5846 -> 0 bytes
-rw-r--r--vignettes/examples-L2_resplot.pdfbin4988 -> 0 bytes
-rw-r--r--vignettes/examples.aux29
-rw-r--r--vignettes/examples.bbl30
-rw-r--r--vignettes/examples.blg46
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-rw-r--r--vignettes/examples.out5
-rw-r--r--vignettes/examples.pdfbin155612 -> 155610 bytes
-rw-r--r--vignettes/examples.tex657
-rw-r--r--vignettes/examples.toc5
-rw-r--r--vignettes/kinfit.pdfbin265975 -> 227085 bytes
15 files changed, 0 insertions, 1389 deletions
diff --git a/vignettes/examples-FOCUS_2006_L3_2.pdf b/vignettes/examples-FOCUS_2006_L3_2.pdf
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diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf
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diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf
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diff --git a/vignettes/examples-L2_plot.pdf b/vignettes/examples-L2_plot.pdf
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diff --git a/vignettes/examples-L2_resplot.pdf b/vignettes/examples-L2_resplot.pdf
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diff --git a/vignettes/examples.aux b/vignettes/examples.aux
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diff --git a/vignettes/examples.bbl b/vignettes/examples.bbl
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-\bibitem[{FOCUS Work Group on Degradation Kinetics}(2006)]{FOCUS2006}
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-\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}.
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-\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[mkin(2013)]{pkg:mkin}
-mkin.
-\newblock \emph{mkin: {R}outines for fitting kinetic models with one or more
- state variables to chemical degradation data}, 2013.
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-\newblock R package version 0.9-11.
-
-\end{thebibliography}
diff --git a/vignettes/examples.blg b/vignettes/examples.blg
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diff --git a/vignettes/examples.log b/vignettes/examples.log
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-\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
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-% $Id: $
-%%\VignetteIndexEntry{Examples for kinetic evaluations using kinfit}
-%%\usepackage{Sweave}
-\documentclass[12pt,a4paper]{article}
-\usepackage{a4wide}
-%%\usepackage[lists,heads]{endfloat}
-\input{header}
-\hypersetup{
- pdftitle = {Examples for kinetic evaluations using kinfit},
- 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 kinfit}
-\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{mkin} package \citep{pkg:mkin}. The datasets are from Appendix 3,
-of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}.
-
-\subsection{Laboratory Data L1}
-
-The following code defines an object containing the example dataset L1 from the
-FOCUS kinetics report, p. 284
-
-\begin{Schunk}
-\begin{Sinput}
-R> library("kinfit")
-R> FOCUS_2006_L1 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L1$data = data.frame(
-+ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
-+ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
-+ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
-+ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
-\end{Sinput}
-\end{Schunk}
-
-The following two lines fit the model and produce the summary report
-of the model fit. This covers the numerical analyses given in the
-FOCUS report.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits)
-R> kinreport(FOCUS_2006_L1)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:07:59 2013
-
-Data:
- t parent
-1 0 88.3
-2 0 91.4
-3 1 85.6
-4 1 84.5
-5 2 78.9
-6 2 77.6
-7 3 72.0
-8 3 71.9
-9 5 50.3
-10 5 59.4
-11 7 47.0
-12 7 45.1
-13 14 27.7
-14 14 27.3
-15 21 10.0
-16 21 10.4
-17 30 2.9
-18 30 4.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 92.4710 1.36830 67.6 0.00e+00
-k 0.0956 0.00388 24.6 1.87e-14
-
-Chi2 error estimation: 3.42 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 7.2 24.1
-\end{Soutput}
-\end{Schunk}
-
-Obviously, the FOMC model and the DFOP model were not fitted. As discussed in the
-kinfit vignette of this package, this occurs when the SFO model fits very well.
-
-We can try to force the FOMC fit using the parameters obtained using mkin.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.FOMC = list(parent.0 = 92.47, alpha = 1.35e11, beta = 1.41e12))
-R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits)
-R> kinreport(FOCUS_2006_L1)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 88.3
-2 0 91.4
-3 1 85.6
-4 1 84.5
-5 2 78.9
-6 2 77.6
-7 3 72.0
-8 3 71.9
-9 5 50.3
-10 5 59.4
-11 7 47.0
-12 7 45.1
-13 14 27.7
-14 14 27.3
-15 21 10.0
-16 21 10.4
-17 30 2.9
-18 30 4.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 92.4710 1.36830 67.6 0.00e+00
-k 0.0956 0.00388 24.6 1.87e-14
-
-Chi2 error estimation: 3.42 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 7.2 24.1
-\end{Soutput}
-\end{Schunk}
-
-It still does not converge. As discussed in the kinfit vignette, the FOMC model usually
-is not returned by kinfit when the SFO model fits very well. This should be seen as
-a feature, not a bug, as the FOMC model is ill-defined in such cases.
-
-A plot of the fit is obtained with the kinplot function.
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L1, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L1_SFO_plot}
-
-The residual plot can be easily obtained by
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinresplot(FOCUS_2006_L1, "SFO", ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L1_SFO_residuals}
-
-\subsection{Laboratory Data L2}
-
-The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L2$data = 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))
-\end{Sinput}
-\end{Schunk}
-
-Again, the SFO, FOMC and DFOP models are fitted and a report is printed.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits)
-R> kinreport(FOCUS_2006_L2)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.1
-2 0 91.8
-3 1 41.4
-4 1 38.7
-5 3 19.3
-6 3 22.3
-7 7 4.6
-8 7 4.6
-9 14 2.6
-10 14 1.2
-11 28 0.3
-12 28 0.6
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 91.466 3.8065 24.03 1.77e-10
-k 0.663 0.0712 9.31 1.52e-06
-
-Chi2 error estimation: 14.38 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 93.77 1.856 50.51 1.17e-12
-alpha 1.37 0.257 5.36 2.30e-04
-beta 1.23 0.363 3.40 3.95e-03
-
-Chi2 error estimation: 6.2 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 1.0 3.5
-FOMC 0.8 5.4
-\end{Soutput}
-\end{Schunk}
-
-Here, only the DFOP did not converge using default parameters. The DFOP fit can be
-obtained using refined starting parameters:
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.DFOP = list(parent.0 = 94, g = 0.4, k1 = 142, k2 = 0.34))
-R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits)
-R> kinreport(FOCUS_2006_L2)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.1
-2 0 91.8
-3 1 41.4
-4 1 38.7
-5 3 19.3
-6 3 22.3
-7 7 4.6
-8 7 4.6
-9 14 2.6
-10 14 1.2
-11 28 0.3
-12 28 0.6
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 91.466 3.8065 24.03 1.77e-10
-k 0.663 0.0712 9.31 1.52e-06
-
-Chi2 error estimation: 14.38 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 93.77 1.856 50.51 1.17e-12
-alpha 1.37 0.257 5.36 2.30e-04
-beta 1.23 0.363 3.40 3.95e-03
-
-Chi2 error estimation: 6.2 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 1.0 3.5
-FOMC 0.8 5.4
-\end{Soutput}
-\end{Schunk}
-
-Again, even with starting parameters very close to the optimum obtained using mkin,
-there is no convergence with kinfit. However, when looking at the fit obtained using
-mkin plotted in the mkin vignette, it is clear that the point where the break point
-of the curve, caused by the large difference between k1 and k2, is not clearly defined
-by the data. Therefore, it should be seen as a desirable feature of the
-underlying nls() function that no solution is returned.
-
-Comparison of $\chi^2$ error levels of the two models shows that the FOMC model allows
-for a better representation of the data. This is also obvious from the plot
-of the fits.
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L2, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L2_plot}
-
-Residual plots are obtained using kinresplot.
-
-\begin{Schunk}
-\begin{Sinput}
-R> par(mfrow=c(2,1))
-R> kinresplot(FOCUS_2006_L2, "SFO", ylab = "Observed")
-R> kinresplot(FOCUS_2006_L2, "FOMC", ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L2_resplot}
-
-\subsection{Laboratory Data L3}
-
-The following code defines example dataset L3 from the FOCUS kinetics
-report, p. 290 and attempts to fit the SFO, FOMC and DFOP models.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L3 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L3$data = data.frame(
-+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
-+ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits)
-R> kinreport(FOCUS_2006_L3)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 97.8
-2 3 60.0
-3 7 51.0
-4 14 43.0
-5 30 35.0
-6 60 22.0
-7 91 15.0
-8 120 12.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 74.8718 8.45736 8.85 5.78e-05
-k 0.0253 0.00824 3.07 1.10e-02
-
-Chi2 error estimation: 21.24 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 97.7460 1.438160 68.0 1.40e-07
-k1 0.5162 0.068841 7.5 8.46e-04
-k2 0.0138 0.000812 16.9 3.56e-05
-g 0.4566 0.017970 25.4 7.12e-06
-
-Chi2 error estimation: 2.22 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 27.4 91.1
-DFOP 7.5 123.0
-\end{Soutput}
-\end{Schunk}
-
-In this case, the FOMC model does not return a solution using kinfit. Trying with
-closer starting parameters gives success this time.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.FOMC = list(parent.0 = 100, alpha = 0.5, beta = 2))
-R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits)
-R> kinreport(FOCUS_2006_L3)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 97.8
-2 3 60.0
-3 7 51.0
-4 14 43.0
-5 30 35.0
-6 60 22.0
-7 91 15.0
-8 120 12.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 74.8718 8.45736 8.85 5.78e-05
-k 0.0253 0.00824 3.07 1.10e-02
-
-Chi2 error estimation: 21.24 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 96.974 4.550 21.31 2.11e-06
-alpha 0.422 0.072 5.87 1.02e-03
-beta 1.858 0.881 2.11 4.44e-02
-
-Chi2 error estimation: 7.32 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 97.7460 1.438160 68.0 1.40e-07
-k1 0.5162 0.068841 7.5 8.46e-04
-k2 0.0138 0.000812 16.9 3.56e-05
-g 0.4566 0.017970 25.4 7.12e-06
-
-Chi2 error estimation: 2.22 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 27.4 91.1
-FOMC 7.7 431.2
-DFOP 7.5 123.0
-\end{Soutput}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L3, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-FOCUS_2006_L3_2}
-
-Based on the $\chi^2$ error level criterion and the visual analysis of the
-fits, the DFOP model would be the best-fit model of choice for laboratory data
-L3.
-
-\subsection{Laboratory Data L4}
-
-The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293 and attempts to fit the SFO, FOMC and DFOP models.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L4 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L4$data = data.frame(
-+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
-+ parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-R> FOCUS_2006_L4$fits <- kinfit(FOCUS_2006_L4$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L4$results <- kinresults(FOCUS_2006_L4$fits)
-R> kinreport(FOCUS_2006_L4)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.6
-2 3 96.3
-3 7 94.3
-4 14 88.8
-5 30 74.9
-6 60 59.9
-7 91 53.5
-8 120 49.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 96.44152 1.948781 49.5 2.28e-09
-k 0.00654 0.000523 12.5 8.01e-06
-
-Chi2 error estimation: 3.29 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 99.143 1.680 59.02 1.32e-08
-alpha 0.704 0.262 2.68 2.18e-02
-beta 64.980 36.617 1.77 6.81e-02
-
-Chi2 error estimation: 2.03 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 98.7514 1.33707 73.857 1.01e-07
-k1 0.0105 0.00449 2.348 3.93e-02
-k2 -0.0112 0.01884 -0.596 7.08e-01
-g 0.9390 0.18530 5.068 3.57e-03
-
-Chi2 error estimation: 1.63 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 106.0 352.0
-FOMC 108.9 1644.1
-DFOP 118.7 122.8
-\end{Soutput}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L4, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-FOCUS_2006_L4}
-
-Although the $\chi^2$ error level is slightly smaller for the DFOP model and also
-for the FOMC model, the differences are small, and the SFO model may appear to
-be a suitable choice. The better fit of the DFOP model depends very much on the
-last three data points.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.toc b/vignettes/examples.toc
deleted file mode 100644
index af3c624..0000000
--- a/vignettes/examples.toc
+++ /dev/null
@@ -1,5 +0,0 @@
-\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}{5}{subsection.1.2}
-\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{10}{subsection.1.3}
-\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{14}{subsection.1.4}
diff --git a/vignettes/kinfit.pdf b/vignettes/kinfit.pdf
index 5fdc7c3..35bb9b8 100644
--- a/vignettes/kinfit.pdf
+++ b/vignettes/kinfit.pdf
Binary files differ

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