Some updates of the mkin vignette

Added the kinfit vignette file to the repository



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@57 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

4 files changed, 90 insertions, 70 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 62c98813..8875c6ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: mkin
 Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
-Version: 0.9-06
-Date: 2012-07-03
+Version: 0.9-07
+Date: 2012-09-20
 Author: Johannes Ranke, Katrin Lindenberger, René Lehmann
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 Description: Calculation routines based on the FOCUS Kinetics Report (2006).
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index 9110ad7f..2f79cc56 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -60,10 +60,10 @@ metabolites.
 

 Many approaches are possible regarding the evaluation of chemical degradation

 data.  The \Rpackage{kinfit} package \citep{pkg:kinfit} in \RR{}

-\citep{rcore2010} implements the approach recommended in the kinetics report

+\citep{rcore2012} implements the approach recommended in the kinetics report

 provided by the FOrum for Co-ordination of pesticide fate models and their

-USe \citep{FOCUS2006} for simple data series for one parent compound in one

-compartment.

+USe \citep{FOCUS2006, FOCUSkinetics2011} for simple data series for one parent

+compound in one compartment.

 

 The \Rpackage{mkin} package \citep{pkg:mkin} extends this approach to data series

 with metabolites and more than one compartment and includes the possibility 

@@ -131,14 +131,14 @@ differential equations. In these cases, a coefficient matrix is also returned.
 

 Other models that include time on the right-hand side of the differential 

 equation are the first-order multi-compartment (FOMC) model and the

-Hockey-Stick (HS) model. At present, only the FOMC model can only be used, and

-only for the parent compound.

+Hockey-Stick (HS) model. At present, these models can only be used only for the

+parent compound.

 

 \subsection{Fitting the model}

 

 Then the model parameters should be fitted to the data. The function

 \Robject{mkinfit} internally creates a cost function using \Robject{modCost}

-from the \Rpackage{FME} package and the produces a fit using \Robject{modFit}

+from the \Rpackage{FME} package and then produces a fit using \Robject{modFit}

 from the same package. In cases of linear first-order differential 

 equations, the solution used for calculating the cost function is based

 on the fundamental system of the coefficient matrix, as proposed by 

diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
new file mode 100644
index 00000000..e1fe3528
--- /dev/null
+++ b/vignettes/mkin.pdf
diff --git a/vignettes/references.bib b/vignettes/references.bib
index 24672e2e..cbd726ce 100644
--- a/vignettes/references.bib
+++ b/vignettes/references.bib
@@ -1,62 +1,82 @@
-@Manual{pkg:kinfit,

-    title = {kinfit: {R}outines for fitting simple kinetic models to chemical degradation data},

-    author = {Johannes Ranke},

-    year = {2010},

-    url = {http://CRAN.R-project.org}

-}

-

-@Manual{pkg:mkin,

-    title = {mkin: {R}outines for fitting kinetic models with one or more state variables to chemical degradation data},

-    author = {Johannes Ranke},

-    year = {2010},

-    url = {http://CRAN.R-project.org}

-}

-

-@Article{soetaert10,

-    title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in {R} Using Package {FME}},

-    author = {Karline Soetaert and Thomas Petzoldt},

-    journal = {Journal of Statistical Software},

-    year = {2010},

-    volume = {33},

-    number = {3},

-    pages = {1--28},

-    url = {http://www.jstatsoft.org/v33/i03/}

-}

-

-@Manual{          rcore2010,

-  title         = {\textsf{R}: A Language and Environment for Statistical

-                  Computing},

-  author        = {{R Development Core Team}},

-  organization  = {R Foundation for Statistical Computing},

-  address       = {Vienna, Austria},

-  year          = 2010,

-  note          = {{ISBN} 3-900051-07-0},

-  url           = {http://www.R-project.org}

-}

-

-@Manual{          FOCUS2006,

-  title         = {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},

-  note          = {EC Document Reference Sanco/10058/2005 version 2.0},

-  author        = {{FOCUS Work Group on Degradation Kinetics}},

-  year          = {2006},

-  url           = {http://focus.jrc.ec.europa.eu/dk} 

-}

-

-@Inproceedings{   schaefer2007,

-  title         = {{KinGUI}: a new kinetic software tool for evaluations according to FOCUS degradation kinetics},

-  author       = {D. Sch\"{a}fer and M. Mikolasch and P. Rainbird and B. Harvey},

-  booktitle    = {Proceedings of the XIII Symposium Pesticide Chemistry},

-  editor       = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.},

-  year          = {2007},

-  address       = {Piacenza},

-  pages         = {916--923}

-}

-

-@Book{            bates88,

-  title         = {Nonlinear regression and its applications},

-  author        = {D. Bates and D. Watts},

-  year          = {1988},

-  publisher     = {Wiley-Interscience}

-}

+% This file was created with JabRef 2.7b.
+% Encoding: ISO8859_1
+
+@BOOK{bates88,
+  title = {Nonlinear regression and its applications},
+  publisher = {Wiley-Interscience},
+  year = {1988},
+  author = {D. Bates and D. Watts}
+}
+
+@MANUAL{FOCUSkinetics2011,
+  title = {Generic guidance for estimating persistence and degradation kinetics
+	from environmental fate studies on pesticides in EU registration},
+  author = {{FOCUS Work Group on Degradation Kinetics}},
+  edition = {1.0},
+  month = {November},
+  year = {2011},
+  file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF},
+  owner = {ranke},
+  timestamp = {2012.09.20},
+  url = {http://focus.jrc.ec.europa.eu/dk}
+}
+
+@MANUAL{FOCUS2006,
+  title = {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},
+  author = {{FOCUS Work Group on Degradation Kinetics}},
+  year = {2006},
+  note = {EC Document Reference Sanco/10058/2005 version 2.0},
+  url = {http://focus.jrc.ec.europa.eu/dk}
+}
+
+@MANUAL{rcore2012,
+  title = {\textsf{R}: A Language and Environment for Statistical Computing},
+  author = {{R Development Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2012},
+  note = {{ISBN} 3-900051-07-0},
+  url = {http://www.R-project.org}
+}
+
+@MANUAL{pkg:kinfit,
+  title = {kinfit: {R}outines for fitting simple kinetic models to chemical
+	degradation data},
+  author = {Johannes Ranke},
+  year = {2012},
+  url = {http://CRAN.R-project.org}
+}
+
+@MANUAL{pkg:mkin,
+  title = {mkin: {R}outines for fitting kinetic models with one or more state
+	variables to chemical degradation data},
+  author = {Johannes Ranke},
+  year = {2012},
+  url = {http://CRAN.R-project.org}
+}
+
+@INPROCEEDINGS{schaefer2007,
+  author = {D. Sch\"{a}fer and M. Mikolasch and P. Rainbird and B. Harvey},
+  title = {{KinGUI}: a new kinetic software tool for evaluations according to
+	FOCUS degradation kinetics},
+  booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry},
+  year = {2007},
+  editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.},
+  pages = {916--923},
+  address = {Piacenza}
+}
+
+@ARTICLE{soetaert10,
+  author = {Karline Soetaert and Thomas Petzoldt},
+  title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in {R} Using
+	Package {FME}},
+  journal = {Journal of Statistical Software},
+  year = {2010},
+  volume = {33},
+  pages = {1--28},
+  number = {3},
+  url = {http://www.jstatsoft.org/v33/i03/}
+}
+