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-rw-r--r--DESCRIPTION4
-rw-r--r--vignettes/mkin.Rnw12
-rw-r--r--vignettes/mkin.pdfbin0 -> 182949 bytes
-rw-r--r--vignettes/references.bib144
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
Binary files differ
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/}
+}
+

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