From d267b8c116f78ee9b7b4d76c9ddb7b8950a127b4 Mon Sep 17 00:00:00 2001 From: jranke Date: Thu, 20 Sep 2012 11:02:28 +0000 Subject: 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 --- DESCRIPTION | 4 +- vignettes/mkin.Rnw | 12 ++-- vignettes/mkin.pdf | Bin 0 -> 182949 bytes vignettes/references.bib | 144 +++++++++++++++++++++++++++-------------------- 4 files changed, 90 insertions(+), 70 deletions(-) create mode 100644 vignettes/mkin.pdf diff --git a/DESCRIPTION b/DESCRIPTION index 62c9881..8875c6e 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 Description: Calculation routines based on the FOCUS Kinetics Report (2006). diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw index 9110ad7..2f79cc5 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 0000000..e1fe352 Binary files /dev/null and b/vignettes/mkin.pdf differ diff --git a/vignettes/references.bib b/vignettes/references.bib index 24672e2..cbd726c 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/} +} + -- cgit v1.2.1