- 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

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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--- a/vignettes/examples-FOCUS_2006_L3_2.pdf
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diff --git a/vignettes/examples-FOCUS_2006_L4.pdf b/vignettes/examples-FOCUS_2006_L4.pdf
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index bd67e70..0000000
--- a/vignettes/examples-FOCUS_2006_L4.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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--- a/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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--- a/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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--- a/vignettes/examples-L2_resplot.pdf
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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}(2011)]{FOCUSkinetics2011}
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-\newblock \emph{Generic guidance for estimating persistence and degradation
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-
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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