- Moved the vignette to the location that is meanwhile recommended

- Update of the vignette
- A bit of cleanup



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@42 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

56 files changed, 16 insertions, 24 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 622a9a0..d310996 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: kinfit

 Type: Package

 Title: Routines for fitting kinetic models to chemical degradation data

-Version: 1.1.06

-Date: 2011-11-09

+Version: 1.1.07

+Date: 2012-06-26

 Author: Johannes Ranke and Katrin Lindenberger

 Maintainer: Johannes Ranke <jranke@users.berlios.de>

 Description: Simple calculation routines based on the FOCUS Kinetics 

@@ -13,4 +13,4 @@ Description: Simple calculation routines based on the FOCUS Kinetics
 License: GPL

 LazyLoad: yes

 LazyData: yes

-URL: http://cran.r-project.org, http://developer.berlios.de/projects/mkin/

+URL: http://cran.r-project.org, http://kinfit.r-forge.r-project.org

diff --git a/data/FOCUS_2006_A_SFO_ref.tex b/data/FOCUS_2006_A_SFO_ref.tex
deleted file mode 100644
index a63cf65..0000000
--- a/data/FOCUS_2006_A_SFO_ref.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-ACSL & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ 

-Excel & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ 

-Kinetica & 109.11 & 0.0371 & 18.66 & 62.00 & A \\ 

-Madonna & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ 

-Mathematica & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ 

-MatLab & 109.15 & 0.0372 & 18.63 & 61.87 & A \\ 

-ModelMaker & 109.10 & 0.0371 & 18.68 & 62.06 & A \\ 

-ModelManager & 109.15 & 0.0372 & 18.62 & 61.86 & A \\ 

-PRISM & 109.20 & 0.0372 & 18.63 & 61.90 & A \\ 

-Statistica & 109.15 & 0.0372 & 18.63 & 61.90 & A \\ 

-Tablecurve & 109.15 & 0.0372 & 18.62 & 61.87 & A \\ 

diff --git a/inst/doc/FOCUS_2006_FOMC_F_total_ref.tex b/inst/doc/FOCUS_2006_FOMC_F_total_ref.tex
deleted file mode 100644
index e69de29..0000000
--- a/inst/doc/FOCUS_2006_FOMC_F_total_ref.tex
+++ /dev/null
diff --git a/inst/doc/run.bat b/inst/doc/run.bat
deleted file mode 100644
index 530c31e..0000000
--- a/inst/doc/run.bat
+++ /dev/null
@@ -1,5 +0,0 @@
-R.exe -e "Sweave('kinfit.Rnw', stylepath=FALSE)"

-pdflatex.exe kinfit

-bibtex.exe kinfit

-pdflatex.exe kinfit

-pdflatex.exe kinfit

diff --git a/tests/test_FOCUS_2006_A.Rout.save b/tests/test_FOCUS_2006_A.Rout.save
index d209084..1b459f6 100644
--- a/tests/test_FOCUS_2006_A.Rout.save
+++ b/tests/test_FOCUS_2006_A.Rout.save
@@ -81,7 +81,7 @@ FOMC 6.9350 24.044
 > print(kinresults(fits)$stats, digits=5)

      n.times df mean.means    RSS  err.min      R2

 SFO        9  7     39.523 207.63 0.064524 0.99194

-FOMC       9  6     39.523 205.45 0.067802 0.99202

+FOMC       9  6     39.523 205.45 0.067792 0.99202

 > 

 > data(FOCUS_2006_E)

 > fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP"))

diff --git a/inst/doc/KinGUI/A_DFOP_report.txt b/vignettes/KinGUI/A_DFOP_report.txt
index b887a46..b887a46 100644
--- a/inst/doc/KinGUI/A_DFOP_report.txt
+++ b/vignettes/KinGUI/A_DFOP_report.txt
diff --git a/inst/doc/KinGUI/A_DFOP_report_detailed.txt b/vignettes/KinGUI/A_DFOP_report_detailed.txt
index 242c1e7..242c1e7 100644
--- a/inst/doc/KinGUI/A_DFOP_report_detailed.txt
+++ b/vignettes/KinGUI/A_DFOP_report_detailed.txt
diff --git a/inst/doc/KinGUI/A_FOMC_report.txt b/vignettes/KinGUI/A_FOMC_report.txt
index dbd9182..dbd9182 100644
--- a/inst/doc/KinGUI/A_FOMC_report.txt
+++ b/vignettes/KinGUI/A_FOMC_report.txt
diff --git a/inst/doc/KinGUI/A_FOMC_report_detailed.txt b/vignettes/KinGUI/A_FOMC_report_detailed.txt
index 2b14a22..2b14a22 100644
--- a/inst/doc/KinGUI/A_FOMC_report_detailed.txt
+++ b/vignettes/KinGUI/A_FOMC_report_detailed.txt
diff --git a/inst/doc/KinGUI/A_HS_report.txt b/vignettes/KinGUI/A_HS_report.txt
index 00c5fef..00c5fef 100644
--- a/inst/doc/KinGUI/A_HS_report.txt
+++ b/vignettes/KinGUI/A_HS_report.txt
diff --git a/inst/doc/KinGUI/A_HS_report_detailed.txt b/vignettes/KinGUI/A_HS_report_detailed.txt
index 9cc5aee..9cc5aee 100644
--- a/inst/doc/KinGUI/A_HS_report_detailed.txt
+++ b/vignettes/KinGUI/A_HS_report_detailed.txt
diff --git a/inst/doc/KinGUI/A_KinGUI.txt b/vignettes/KinGUI/A_KinGUI.txt
index f42b72c..f42b72c 100644
--- a/inst/doc/KinGUI/A_KinGUI.txt
+++ b/vignettes/KinGUI/A_KinGUI.txt
diff --git a/inst/doc/KinGUI/A_SFO_report.txt b/vignettes/KinGUI/A_SFO_report.txt
index 8ee2968..8ee2968 100644
--- a/inst/doc/KinGUI/A_SFO_report.txt
+++ b/vignettes/KinGUI/A_SFO_report.txt
diff --git a/inst/doc/KinGUI/A_SFO_report_detailed.txt b/vignettes/KinGUI/A_SFO_report_detailed.txt
index 98e5979..98e5979 100644
--- a/inst/doc/KinGUI/A_SFO_report_detailed.txt
+++ b/vignettes/KinGUI/A_SFO_report_detailed.txt
diff --git a/inst/doc/KinGUI/B_DFOP_report.txt b/vignettes/KinGUI/B_DFOP_report.txt
index 0ee160b..0ee160b 100644
--- a/inst/doc/KinGUI/B_DFOP_report.txt
+++ b/vignettes/KinGUI/B_DFOP_report.txt
diff --git a/inst/doc/KinGUI/B_DFOP_report_detailed.txt b/vignettes/KinGUI/B_DFOP_report_detailed.txt
index e30f7b1..e30f7b1 100644
--- a/inst/doc/KinGUI/B_DFOP_report_detailed.txt
+++ b/vignettes/KinGUI/B_DFOP_report_detailed.txt
diff --git a/inst/doc/KinGUI/B_FOMC_report.txt b/vignettes/KinGUI/B_FOMC_report.txt
index 1a1db57..1a1db57 100644
--- a/inst/doc/KinGUI/B_FOMC_report.txt
+++ b/vignettes/KinGUI/B_FOMC_report.txt
diff --git a/inst/doc/KinGUI/B_FOMC_report_detailed.txt b/vignettes/KinGUI/B_FOMC_report_detailed.txt
index 449ab34..449ab34 100644
--- a/inst/doc/KinGUI/B_FOMC_report_detailed.txt
+++ b/vignettes/KinGUI/B_FOMC_report_detailed.txt
diff --git a/inst/doc/KinGUI/B_HS_report.txt b/vignettes/KinGUI/B_HS_report.txt
index 18bb818..18bb818 100644
--- a/inst/doc/KinGUI/B_HS_report.txt
+++ b/vignettes/KinGUI/B_HS_report.txt
diff --git a/inst/doc/KinGUI/B_HS_report_detailed.txt b/vignettes/KinGUI/B_HS_report_detailed.txt
index f723ea4..f723ea4 100644
--- a/inst/doc/KinGUI/B_HS_report_detailed.txt
+++ b/vignettes/KinGUI/B_HS_report_detailed.txt
diff --git a/inst/doc/KinGUI/B_KinGUI.txt b/vignettes/KinGUI/B_KinGUI.txt
index 6a589b2..6a589b2 100644
--- a/inst/doc/KinGUI/B_KinGUI.txt
+++ b/vignettes/KinGUI/B_KinGUI.txt
diff --git a/inst/doc/KinGUI/B_SFO_report.txt b/vignettes/KinGUI/B_SFO_report.txt
index d3856fe..d3856fe 100644
--- a/inst/doc/KinGUI/B_SFO_report.txt
+++ b/vignettes/KinGUI/B_SFO_report.txt
diff --git a/inst/doc/KinGUI/B_SFO_report_detailed.txt b/vignettes/KinGUI/B_SFO_report_detailed.txt
index ff6e9c8..ff6e9c8 100644
--- a/inst/doc/KinGUI/B_SFO_report_detailed.txt
+++ b/vignettes/KinGUI/B_SFO_report_detailed.txt
diff --git a/inst/doc/KinGUI/C_DFOP_report.txt b/vignettes/KinGUI/C_DFOP_report.txt
index 65b8f29..65b8f29 100644
--- a/inst/doc/KinGUI/C_DFOP_report.txt
+++ b/vignettes/KinGUI/C_DFOP_report.txt
diff --git a/inst/doc/KinGUI/C_DFOP_report_detailed.txt b/vignettes/KinGUI/C_DFOP_report_detailed.txt
index b26c063..b26c063 100644
--- a/inst/doc/KinGUI/C_DFOP_report_detailed.txt
+++ b/vignettes/KinGUI/C_DFOP_report_detailed.txt
diff --git a/inst/doc/KinGUI/C_FOMC_report.txt b/vignettes/KinGUI/C_FOMC_report.txt
index 3d74181..3d74181 100644
--- a/inst/doc/KinGUI/C_FOMC_report.txt
+++ b/vignettes/KinGUI/C_FOMC_report.txt
diff --git a/inst/doc/KinGUI/C_FOMC_report_detailed.txt b/vignettes/KinGUI/C_FOMC_report_detailed.txt
index f19484c..f19484c 100644
--- a/inst/doc/KinGUI/C_FOMC_report_detailed.txt
+++ b/vignettes/KinGUI/C_FOMC_report_detailed.txt
diff --git a/inst/doc/KinGUI/C_HS_report.txt b/vignettes/KinGUI/C_HS_report.txt
index ca137d4..ca137d4 100644
--- a/inst/doc/KinGUI/C_HS_report.txt
+++ b/vignettes/KinGUI/C_HS_report.txt
diff --git a/inst/doc/KinGUI/C_HS_report_detailed.txt b/vignettes/KinGUI/C_HS_report_detailed.txt
index b8a5753..b8a5753 100644
--- a/inst/doc/KinGUI/C_HS_report_detailed.txt
+++ b/vignettes/KinGUI/C_HS_report_detailed.txt
diff --git a/inst/doc/KinGUI/C_KinGUI.txt b/vignettes/KinGUI/C_KinGUI.txt
index 1e0e3d8..1e0e3d8 100644
--- a/inst/doc/KinGUI/C_KinGUI.txt
+++ b/vignettes/KinGUI/C_KinGUI.txt
diff --git a/inst/doc/KinGUI/C_SFO_report.txt b/vignettes/KinGUI/C_SFO_report.txt
index 5e32b0b..5e32b0b 100644
--- a/inst/doc/KinGUI/C_SFO_report.txt
+++ b/vignettes/KinGUI/C_SFO_report.txt
diff --git a/inst/doc/KinGUI/C_SFO_report_detailed.txt b/vignettes/KinGUI/C_SFO_report_detailed.txt
index 512e10e..512e10e 100644
--- a/inst/doc/KinGUI/C_SFO_report_detailed.txt
+++ b/vignettes/KinGUI/C_SFO_report_detailed.txt
diff --git a/inst/doc/KinGUI/D_DFOP_report.txt b/vignettes/KinGUI/D_DFOP_report.txt
index 31ab25d..31ab25d 100644
--- a/inst/doc/KinGUI/D_DFOP_report.txt
+++ b/vignettes/KinGUI/D_DFOP_report.txt
diff --git a/inst/doc/KinGUI/D_DFOP_report_detailed.txt b/vignettes/KinGUI/D_DFOP_report_detailed.txt
index 8326b6b..8326b6b 100644
--- a/inst/doc/KinGUI/D_DFOP_report_detailed.txt
+++ b/vignettes/KinGUI/D_DFOP_report_detailed.txt
diff --git a/inst/doc/KinGUI/D_FOMC_report.txt b/vignettes/KinGUI/D_FOMC_report.txt
index a2a60f9..a2a60f9 100644
--- a/inst/doc/KinGUI/D_FOMC_report.txt
+++ b/vignettes/KinGUI/D_FOMC_report.txt
diff --git a/inst/doc/KinGUI/D_FOMC_report_detailed.txt b/vignettes/KinGUI/D_FOMC_report_detailed.txt
index a3ff6cc..a3ff6cc 100644
--- a/inst/doc/KinGUI/D_FOMC_report_detailed.txt
+++ b/vignettes/KinGUI/D_FOMC_report_detailed.txt
diff --git a/inst/doc/KinGUI/D_HS_report.txt b/vignettes/KinGUI/D_HS_report.txt
index 92186cd..92186cd 100644
--- a/inst/doc/KinGUI/D_HS_report.txt
+++ b/vignettes/KinGUI/D_HS_report.txt
diff --git a/inst/doc/KinGUI/D_HS_report_detailed.txt b/vignettes/KinGUI/D_HS_report_detailed.txt
index 6f9030e..6f9030e 100644
--- a/inst/doc/KinGUI/D_HS_report_detailed.txt
+++ b/vignettes/KinGUI/D_HS_report_detailed.txt
diff --git a/inst/doc/KinGUI/D_KinGUI.txt b/vignettes/KinGUI/D_KinGUI.txt
index f1c53e9..f1c53e9 100644
--- a/inst/doc/KinGUI/D_KinGUI.txt
+++ b/vignettes/KinGUI/D_KinGUI.txt
diff --git a/inst/doc/KinGUI/D_SFO_report.txt b/vignettes/KinGUI/D_SFO_report.txt
index 902decf..902decf 100644
--- a/inst/doc/KinGUI/D_SFO_report.txt
+++ b/vignettes/KinGUI/D_SFO_report.txt
diff --git a/inst/doc/KinGUI/D_SFO_report_detailed.txt b/vignettes/KinGUI/D_SFO_report_detailed.txt
index 24ace5f..24ace5f 100644
--- a/inst/doc/KinGUI/D_SFO_report_detailed.txt
+++ b/vignettes/KinGUI/D_SFO_report_detailed.txt
diff --git a/inst/doc/KinGUI/F_system_DFOP_report.txt b/vignettes/KinGUI/F_system_DFOP_report.txt
index 9ec5931..9ec5931 100644
--- a/inst/doc/KinGUI/F_system_DFOP_report.txt
+++ b/vignettes/KinGUI/F_system_DFOP_report.txt
diff --git a/inst/doc/KinGUI/F_system_FOMC_report.txt b/vignettes/KinGUI/F_system_FOMC_report.txt
index 9eb0651..9eb0651 100644
--- a/inst/doc/KinGUI/F_system_FOMC_report.txt
+++ b/vignettes/KinGUI/F_system_FOMC_report.txt
diff --git a/inst/doc/KinGUI/F_system_HS_report.txt b/vignettes/KinGUI/F_system_HS_report.txt
index 81546c7..81546c7 100644
--- a/inst/doc/KinGUI/F_system_HS_report.txt
+++ b/vignettes/KinGUI/F_system_HS_report.txt
diff --git a/inst/doc/KinGUI/F_system_KinGUI.txt b/vignettes/KinGUI/F_system_KinGUI.txt
index 92bd722..92bd722 100644
--- a/inst/doc/KinGUI/F_system_KinGUI.txt
+++ b/vignettes/KinGUI/F_system_KinGUI.txt
diff --git a/inst/doc/KinGUI/F_system_SFO_report.txt b/vignettes/KinGUI/F_system_SFO_report.txt
index 7dffe34..7dffe34 100644
--- a/inst/doc/KinGUI/F_system_SFO_report.txt
+++ b/vignettes/KinGUI/F_system_SFO_report.txt
diff --git a/inst/doc/KinGUI/F_water_DFOP_report.txt b/vignettes/KinGUI/F_water_DFOP_report.txt
index c8275d9..c8275d9 100644
--- a/inst/doc/KinGUI/F_water_DFOP_report.txt
+++ b/vignettes/KinGUI/F_water_DFOP_report.txt
diff --git a/inst/doc/KinGUI/F_water_FOMC_report.txt b/vignettes/KinGUI/F_water_FOMC_report.txt
index 6604e72..6604e72 100644
--- a/inst/doc/KinGUI/F_water_FOMC_report.txt
+++ b/vignettes/KinGUI/F_water_FOMC_report.txt
diff --git a/inst/doc/KinGUI/F_water_HS_report.txt b/vignettes/KinGUI/F_water_HS_report.txt
index 3cda8e3..3cda8e3 100644
--- a/inst/doc/KinGUI/F_water_HS_report.txt
+++ b/vignettes/KinGUI/F_water_HS_report.txt
diff --git a/inst/doc/KinGUI/F_water_KinGUI.txt b/vignettes/KinGUI/F_water_KinGUI.txt
index ce3611d..ce3611d 100644
--- a/inst/doc/KinGUI/F_water_KinGUI.txt
+++ b/vignettes/KinGUI/F_water_KinGUI.txt
diff --git a/inst/doc/KinGUI/F_water_SFO_report.txt b/vignettes/KinGUI/F_water_SFO_report.txt
index 9927133..9927133 100644
--- a/inst/doc/KinGUI/F_water_SFO_report.txt
+++ b/vignettes/KinGUI/F_water_SFO_report.txt
diff --git a/inst/doc/Rplots.pdf b/vignettes/Rplots.pdf
index c52b7ab..c52b7ab 100644
--- a/inst/doc/Rplots.pdf
+++ b/vignettes/Rplots.pdf
diff --git a/inst/doc/header.tex b/vignettes/header.tex
index 9d6ec49..9d6ec49 100644
--- a/inst/doc/header.tex
+++ b/vignettes/header.tex
diff --git a/inst/doc/kinfit.Rnw b/vignettes/kinfit.Rnw
index 3292fd1..7907979 100644
--- a/inst/doc/kinfit.Rnw
+++ b/vignettes/kinfit.Rnw
@@ -26,11 +26,13 @@ options(SweaveHooks = list(
 \begin{document}

 \title{kinfit -\\

 Routines for fitting kinetic models to chemical degradation data}

-\author{\textbf{Johannes Ranke} \\

+\author{\textbf{Johannes Ranke} \\[0.5cm]

 %EndAName

-Product Safety \\

-Harlan Laboratories Ltd. \\

-Zelgliweg 1, CH--4452 Itingen, Switzerland}

+Eurofins Regulatory AG\\

+Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm]

+and\\[0.5cm]

+University of Bremen\\

+}

 \maketitle

 

 \begin{abstract}

@@ -1004,6 +1006,12 @@ with other packages, except for some cases where \Rpackage{kinfit} does not
 produce results and the results obtained with other software packages are

 strongly divergent. 

 

+\section{Acknowledgements}

+

+This package would not have been written without me being introduced to regulatory

+fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd

+(formerly RCC Ltd). Parts of the package were written during my employment at Harlan.

+

 \bibliographystyle{plainnat}

 \bibliography{references}

 

diff --git a/inst/doc/kinfit.pdf b/vignettes/kinfit.pdf
index 0b83a62..1128f91 100644
--- a/inst/doc/kinfit.pdf
+++ b/vignettes/kinfit.pdf
diff --git a/inst/doc/references.bib b/vignettes/references.bib
index 8cde4bd..8cde4bd 100644
--- a/inst/doc/references.bib
+++ b/vignettes/references.bib