diff options
| author | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2013-02-16 21:15:52 +0000 |
|---|---|---|
| committer | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2013-02-16 21:15:52 +0000 |
| commit | 329dadc5fd557cbeec0d1f3a6db57b6b4d6f41d4 (patch) | |
| tree | 8159a9ba673fc6c150a92748e142697c845ece1d /vignettes | |
| parent | e6ba7af29db678ef437e7f8301299ec18f4c66a4 (diff) | |
- Some maintenance fixes
- Start of the examples vignette
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@61 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'vignettes')
22 files changed, 2047 insertions, 0 deletions
diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf Binary files differnew file mode 100644 index 00000000..d4f88349 --- /dev/null +++ b/vignettes/examples-L1_SFO_plot.pdf diff --git a/vignettes/examples-L1_SFO_plots.pdf b/vignettes/examples-L1_SFO_plots.pdf Binary files differnew file mode 100644 index 00000000..d34116fe --- /dev/null +++ b/vignettes/examples-L1_SFO_plots.pdf diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf Binary files differnew file mode 100644 index 00000000..35907df8 --- /dev/null +++ b/vignettes/examples-L1_SFO_residuals.pdf diff --git a/vignettes/examples-L2_DFOP.pdf b/vignettes/examples-L2_DFOP.pdf Binary files differnew file mode 100644 index 00000000..8bbfdf60 --- /dev/null +++ b/vignettes/examples-L2_DFOP.pdf diff --git a/vignettes/examples-L2_DFOP_2.pdf b/vignettes/examples-L2_DFOP_2.pdf Binary files differnew file mode 100644 index 00000000..3437f5da --- /dev/null +++ b/vignettes/examples-L2_DFOP_2.pdf diff --git a/vignettes/examples-L2_FOMC.pdf b/vignettes/examples-L2_FOMC.pdf Binary files differnew file mode 100644 index 00000000..763d6175 --- /dev/null +++ b/vignettes/examples-L2_FOMC.pdf diff --git a/vignettes/examples-L2_SFO_plot.pdf b/vignettes/examples-L2_SFO_plot.pdf Binary files differnew file mode 100644 index 00000000..c8831b91 --- /dev/null +++ b/vignettes/examples-L2_SFO_plot.pdf diff --git a/vignettes/examples-L2_SFO_residuals.pdf b/vignettes/examples-L2_SFO_residuals.pdf Binary files differnew file mode 100644 index 00000000..d56b0d18 --- /dev/null +++ b/vignettes/examples-L2_SFO_residuals.pdf diff --git a/vignettes/examples-L3_DFOP.pdf b/vignettes/examples-L3_DFOP.pdf Binary files differnew file mode 100644 index 00000000..c747d793 --- /dev/null +++ b/vignettes/examples-L3_DFOP.pdf diff --git a/vignettes/examples-L3_FOMC.pdf b/vignettes/examples-L3_FOMC.pdf Binary files differnew file mode 100644 index 00000000..322dbeb0 --- /dev/null +++ b/vignettes/examples-L3_FOMC.pdf diff --git a/vignettes/examples-L3_SFO.pdf b/vignettes/examples-L3_SFO.pdf Binary files differnew file mode 100644 index 00000000..7057333b --- /dev/null +++ b/vignettes/examples-L3_SFO.pdf diff --git a/vignettes/examples-L4_FOMC.pdf b/vignettes/examples-L4_FOMC.pdf Binary files differnew file mode 100644 index 00000000..3f164e79 --- /dev/null +++ b/vignettes/examples-L4_FOMC.pdf diff --git a/vignettes/examples-L4_SFO.pdf b/vignettes/examples-L4_SFO.pdf Binary files differnew file mode 100644 index 00000000..42cdf341 --- /dev/null +++ b/vignettes/examples-L4_SFO.pdf diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw new file mode 100644 index 00000000..24e1b57c --- /dev/null +++ b/vignettes/examples.Rnw @@ -0,0 +1,289 @@ +% $Id: examples.Rnw 66 2010-09-03 08:50:26Z jranke $
+%%\VignetteIndexEntry{Examples for kinetic evaluations using mkin}
+%%VignetteDepends{FME}
+%%\usepackage{Sweave}
+\documentclass[12pt,a4paper]{article}
+\usepackage{a4wide}
+%%\usepackage[lists,heads]{endfloat}
+\input{header}
+\hypersetup{
+ pdftitle = {Examples for kinetic evaluations using mkin},
+ pdfsubject = {Manuscript},
+ pdfauthor = {Johannes Ranke},
+ colorlinks = {true},
+ linkcolor = {blue},
+ citecolor = {blue},
+ urlcolor = {red},
+ hyperindex = {true},
+ linktocpage = {true},
+}
+\SweaveOpts{engine=R, eps=FALSE, keep.source = TRUE}
+<<setup, echo = FALSE, results = hide>>=
+options(prompt = "R> ")
+options(SweaveHooks = list(
+ cex = function() par(cex.lab = 1.3, cex.axis = 1.3)))
+@
+\begin{document}
+\title{Examples for kinetic evaluations using mkin}
+\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{kinfit} package \citep{pkg:kinfit}. The datasets are from Appendix 3,
+of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}.
+
+\subsection{Laboratory Data L1}
+
+The following code defines example dataset L1 from the FOCUS kinetics
+report, p. 284
+
+<<FOCUS_2006_L1_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L1 = 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))
+FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
+@
+
+The next step is to set up the models used for the kinetic analysis. Note that
+the model definitions contain the names of the observed variables in the data.
+In this case, there is only one variable called \Robject{parent}.
+
+<<Simple_models, echo=TRUE>>=
+SFO <- mkinmod(parent = list(type = "SFO"))
+FOMC <- mkinmod(parent = list(type = "FOMC"))
+DFOP <- mkinmod(parent = list(type = "DFOP"))
+@
+
+The three models cover the first assumption of simple first order (SFO),
+the case of declining rate constant over time (FOMC) and the case of two
+different phases of the kinetics (DFOP). For a more detailed discussion
+of the models, please see the FOCUS kinetics report.
+
+The following two lines fit the model and produce the summary report
+of the model fit. This covers the numerical analysis given in the
+FOCUS report.
+
+<<L1_SFO, echo=TRUE>>=
+m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
+summary(m.L1.SFO)
+@
+
+A plot of the fit is obtained with the plot function for mkinfit objects.
+
+<<L1_SFO_plot, fig=TRUE, echo=TRUE>>=
+plot(m.L1.SFO)
+@
+
+The residual plot can be easily obtained by
+
+<<L1_SFO_residuals, fig=TRUE, echo=TRUE>>=
+mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
+@
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+<<L1_FOMC, echo=TRUE>>=
+m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
+s.m.L1.FOMC <- summary(m.L1.FOMC)
+s.m.L1.FOMC$errmin
+@
+
+Due to the higher number of parameters, and the lower number of degrees of freedom
+of the fit, the $\chi^2$ error level is actually higher for the FOMC model (3.6\%) than
+for the SFO model (3.4\%).
+
+\subsection{Laboratory Data L2}
+
+The following code defines example dataset L2 from the FOCUS kinetics
+report, p. 287
+
+<<FOCUS_2006_L2_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L2 = 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))
+FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
+@
+
+Again, the SFO model is fitted and a summary is obtained.
+
+<<L2_SFO, echo=TRUE>>=
+m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
+summary(m.L2.SFO)
+@
+
+The $\chi^2$ error level of 14\% suggests that the model does not fit very well.
+This is also obvious from the plots of the fit and the residuals.
+
+<<L2_SFO_plot, fig=TRUE, echo=TRUE>>=
+plot(m.L2.SFO)
+@
+
+In the FOCUS kinetics report, it is stated that there is no apparent systematic
+error observed from the residual plot up to the measured DT90 (approximately at
+day 5), and there is an underestimation beyond that point.
+
+<<L2_SFO_residuals, fig=TRUE, echo=TRUE>>=
+mkinresplot(m.L2.SFO, ylab = "Observed", xlab = "Time")
+@
+
+We may add that it is difficult to judge the random nature of the residuals just
+from the three samplings at days 0, 1 and 3. Also, it is not clear why a
+consistent underestimation after the approximate DT90 should be irrelevant.
+
+For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level
+is checked.
+
+<<L2_FOMC, echo=TRUE, fig=TRUE>>=
+m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet=TRUE)
+plot(m.L2.FOMC)
+s.m.L2.FOMC <- summary(m.L2.FOMC)
+s.m.L2.FOMC$errmin
+@
+
+The error level at which the $\chi^2$ test passes is much lower in this case.
+Therefore, the FOMC model provides a better description of the data, as less
+experimental error has to be assumed in order to explain the data.
+
+Fitting the four parameter DFOP model does not further reduce the
+$\chi^2$ error level.
+
+<<L2_DFOP, echo=TRUE, fig=TRUE>>=
+m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet=TRUE)
+plot(m.L2.DFOP)
+@
+
+Here, the default starting parameters for the DFOP model obviously do not lead
+to a reasonable solution. Therefore the fit is repeated with different starting
+parameters.
+
+<<L2_DFOP_2, echo=TRUE, fig=TRUE>>=
+m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
+ parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
+ quiet=TRUE)
+plot(m.L2.DFOP)
+summary(m.L2.DFOP)
+s.m.L2.DFOP <- summary(m.L2.DFOP)
+s.m.L2.DFOP$errmin
+@
+
+Therefore, the FOMC model is clearly the best-fit model based on the
+$\chi^2$ error level criterion.
+
+\subsection{Laboratory Data L3}
+
+The following code defines example dataset L3 from the FOCUS kinetics
+report, p. 290
+
+<<FOCUS_2006_L3_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L3 = data.frame(
+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
+ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
+FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
+@
+
+SFO model, summary and plot:
+
+<<L3_SFO, echo=TRUE, fig=TRUE>>=
+m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet=TRUE)
+summary(m.L3.SFO)
+plot(m.L3.SFO)
+@
+
+The $\chi^2$ error level of 22\% as well as the plot suggest that the model
+does not fit very well.
+
+The FOMC model performs better:
+
+<<L3_FOMC, echo=TRUE, fig=TRUE>>=
+m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet=TRUE)
+plot(m.L3.FOMC)
+s.m.L3.FOMC <- summary(m.L3.FOMC)
+s.m.L3.FOMC$errmin
+endpoints(m.L3.FOMC)
+@
+
+The error level at which the $\chi^2$ test passes is 7\% in this case.
+
+Fitting the four parameter DFOP model further reduces the $\chi^2$ error level
+considerably:
+
+<<L3_DFOP, echo=TRUE, fig=TRUE>>=
+m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet=TRUE)
+plot(m.L3.DFOP)
+s.m.L3.DFOP <- summary(m.L3.DFOP)
+s.m.L3.DFOP$errmin
+@
+
+Therefore, the DFOP model is the best-fit model based on the $\chi^2$ error
+level criterion for laboratory data L3.
+
+\subsection{Laboratory Data L4}
+
+The following code defines example dataset L4 from the FOCUS kinetics
+report, p. 293
+
+<<FOCUS_2006_L4_data, echo=TRUE, eval=TRUE>>=
+library("mkin")
+FOCUS_2006_L4 = 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))
+FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
+@
+
+SFO model, summary and plot:
+
+<<L4_SFO, echo=TRUE, fig=TRUE>>=
+m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet=TRUE)
+summary(m.L4.SFO)
+plot(m.L4.SFO)
+@
+
+The $\chi^2$ error level of 3.3\% as well as the plot suggest that the model
+fits very well.
+
+The FOMC model for comparison
+
+<<L4_FOMC, echo=TRUE, fig=TRUE>>=
+m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet=TRUE)
+plot(m.L4.FOMC)
+s.m.L4.FOMC <- summary(m.L4.FOMC)
+s.m.L4.FOMC$errmin
+@
+
+The error level at which the $\chi^2$ test passes is slightly lower for the FOMC
+model. However, the difference appears negligible.
+
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+\end{document}
+% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.aux b/vignettes/examples.aux new file mode 100644 index 00000000..37703381 --- /dev/null +++ b/vignettes/examples.aux @@ -0,0 +1,29 @@ +\relax +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\citation{pkg:kinfit} +\citation{FOCUS2006,FOCUSkinetics2011} +\@writefile{toc}{\contentsline {section}{\numberline {1}Kinetic evaluations for parent compounds}{1}{section.1}} +\newlabel{intro}{{1}{1}{Kinetic evaluations for parent compounds\relax }{section.1}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Laboratory Data L1}{1}{subsection.1.1}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Laboratory Data L2}{6}{subsection.1.2}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{14}{subsection.1.3}} +\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{20}{subsection.1.4}} +\bibstyle{plainnat} +\bibdata{references} +\bibcite{FOCUS2006}{{1}{2006}{{FOCUS Work Group on Degradation Kinetics}}{{}}} +\bibcite{FOCUSkinetics2011}{{2}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}} +\bibcite{pkg:kinfit}{{3}{2012}{{Ranke}}{{}}} diff --git a/vignettes/examples.bbl b/vignettes/examples.bbl new file mode 100644 index 00000000..3f240cf1 --- /dev/null +++ b/vignettes/examples.bbl @@ -0,0 +1,29 @@ +\begin{thebibliography}{3} +\providecommand{\natexlab}[1]{#1} +\providecommand{\url}[1]{\texttt{#1}} +\expandafter\ifx\csname urlstyle\endcsname\relax + \providecommand{\doi}[1]{doi: #1}\else + \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi + +\bibitem[{FOCUS Work Group on Degradation Kinetics}(2006)]{FOCUS2006} +{FOCUS Work Group on Degradation Kinetics}. +\newblock \emph{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}, 2006. +\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}. +\newblock EC Document Reference Sanco/10058/2005 version 2.0. + +\bibitem[{FOCUS Work Group on Degradation Kinetics}(2011)]{FOCUSkinetics2011} +{FOCUS Work Group on Degradation Kinetics}. +\newblock \emph{Generic guidance for estimating persistence and degradation + kinetics from environmental fate studies on pesticides in EU registration}, + 1.0 edition, November 2011. +\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}. + +\bibitem[Ranke(2012)]{pkg:kinfit} +Johannes Ranke. +\newblock \emph{kinfit: {R}outines for fitting simple kinetic models to + chemical degradation data}, 2012. +\newblock URL \url{http://CRAN.R-project.org}. + +\end{thebibliography} diff --git a/vignettes/examples.blg b/vignettes/examples.blg new file mode 100644 index 00000000..61ca3d2c --- /dev/null +++ b/vignettes/examples.blg @@ -0,0 +1,46 @@ +This is BibTeX, Version 0.99d (TeX Live 2012/Debian) +Capacity: max_strings=35307, hash_size=35307, hash_prime=30011 +The top-level auxiliary file: examples.aux +The style file: plainnat.bst +Database file #1: references.bib +You've used 3 entries, + 2773 wiz_defined-function locations, + 609 strings with 5481 characters, +and the built_in function-call counts, 895 in all, are: += -- 82 +> -- 30 +< -- 3 ++ -- 12 +- -- 9 +* -- 57 +:= -- 151 +add.period$ -- 10 +call.type$ -- 3 +change.case$ -- 10 +chr.to.int$ -- 3 +cite$ -- 6 +duplicate$ -- 51 +empty$ -- 76 +format.name$ -- 12 +if$ -- 173 +int.to.chr$ -- 1 +int.to.str$ -- 1 +missing$ -- 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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 diff --git a/vignettes/examples.pdf b/vignettes/examples.pdf Binary files differnew file mode 100644 index 00000000..be0d96e5 --- /dev/null +++ b/vignettes/examples.pdf diff --git a/vignettes/examples.tex b/vignettes/examples.tex new file mode 100644 index 00000000..4f59aa24 --- /dev/null +++ b/vignettes/examples.tex @@ -0,0 +1,700 @@ +% $Id: examples.Rnw 66 2010-09-03 08:50:26Z jranke $ +%%\VignetteIndexEntry{Examples for kinetic evaluations using mkin} +%%VignetteDepends{FME} +%%\usepackage{Sweave} +\documentclass[12pt,a4paper]{article} +\usepackage{a4wide} +%%\usepackage[lists,heads]{endfloat} +\input{header} +\hypersetup{ + pdftitle = {Examples for kinetic evaluations using mkin}, + 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 mkin} +\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{kinfit} package \citep{pkg:kinfit}. The datasets are from Appendix 3, +of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}. + +\subsection{Laboratory Data L1} + +The following code defines example dataset L1 from the FOCUS kinetics +report, p. 284 + +\begin{Schunk} +\begin{Sinput} +R> library("mkin") +R> FOCUS_2006_L1 = 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)) +R> FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) +\end{Sinput} +\end{Schunk} + +The next step is to set up the models used for the kinetic analysis. Note that +the model definitions contain the names of the observed variables in the data. +In this case, there is only one variable called \Robject{parent}. + +\begin{Schunk} +\begin{Sinput} +R> SFO <- mkinmod(parent = list(type = "SFO")) +R> FOMC <- mkinmod(parent = list(type = "FOMC")) +R> DFOP <- mkinmod(parent = list(type = "DFOP")) +\end{Sinput} +\end{Schunk} + +The three models cover the first assumption of simple first order (SFO), +the case of declining rate constant over time (FOMC) and the case of two +different phases of the kinetics (DFOP). For a more detailed discussion +of the models, please see the FOCUS kinetics report. + +The following two lines fit the model and produce the summary report +of the model fit. This covers the numerical analysis given in the +FOCUS report. + +\begin{Schunk} +\begin{Sinput} +R> m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE) +R> summary(m.L1.SFO) +\end{Sinput} +\begin{Soutput} +mkin version: 0.9.10 +R version: 2.15.2 +Date of fit: Sat Feb 16 21:38:15 2013 +Date of summary: Sat Feb 16 21:38:15 2013 + +Equations: +[1] d_parent = - k_parent_sink * parent + +Starting values for optimised parameters: + initial type transformed +parent_0 100.0 state 100.000000 +k_parent_sink 0.1 deparm -2.302585 + +Fixed parameter values: +None + +Optimised, transformed parameters: + Estimate Std. Error +parent_0 92.471 1.368 +k_parent_sink -2.347 0.041 + +Backtransformed parameters: + Estimate +parent_0 92.471 +k_parent_sink 0.096 + +Residual standard error: 2.948 on 16 degrees of freedom + +Chi2 error levels in percent: + err.min n.optim df +All data 3.424 2 7 +parent 3.424 2 7 + +Estimated disappearance times: + DT50 DT90 +parent 7.249 24.08 + +Estimated formation fractions: + ff +parent_sink 1 + +Parameter correlation: + parent_0 k_parent_sink +parent_0 1.0000 0.6248 +k_parent_sink 0.6248 1.0000 + +Data: + time variable observed predicted residual + 0 parent 88.3 92.471 -4.1710 + 0 parent 91.4 92.471 -1.0710 + 1 parent 85.6 84.039 1.5610 + 1 parent 84.5 84.039 0.4610 + 2 parent 78.9 76.376 2.5241 + 2 parent 77.6 76.376 1.2241 + 3 parent 72.0 69.412 2.5884 + 3 parent 71.9 69.412 2.4884 + 5 parent 50.3 57.330 -7.0301 + 5 parent 59.4 57.330 2.0699 + 7 parent 47.0 47.352 -0.3515 + 7 parent 45.1 47.352 -2.2515 + 14 parent 27.7 24.247 3.4527 + 14 parent 27.3 24.247 3.0527 + 21 parent 10.0 12.416 -2.4163 + 21 parent 10.4 12.416 -2.0163 + 30 parent 2.9 5.251 -2.3513 + 30 parent 4.0 5.251 -1.2513 +\end{Soutput} +\end{Schunk} + +A plot of the fit is obtained with the plot function for mkinfit objects. + +\begin{Schunk} +\begin{Sinput} +R> plot(m.L1.SFO) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L1_SFO_plot} + +The residual plot can be obtained using the information contained in the +mkinfit object, which is in fact a derivative of an modFit object defined by +the \Rpackage{FME} package. + +\begin{Schunk} +\begin{Sinput} +R> plot(m.L1.SFO$data$time, m.L1.SFO$data$residual, ++ xlab = "Time", ylab = "Residual", ylim = c(-8, 8)) +R> abline(h = 0, lty = 2) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L1_SFO_residuals} + +For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level +is checked. + +\begin{Schunk} +\begin{Sinput} +R> m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE) +R> s.m.L1.FOMC <- summary(m.L1.FOMC) +R> s.m.L1.FOMC$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.03618911 3 6 +parent 0.03618911 3 6 +\end{Soutput} +\end{Schunk} + +Due to the higher number of parameters, and the lower number of degrees of freedom +of the fit, the $\chi^2$ error level is actually higher for the FOMC model (3.6\%) than +for the SFO model (3.4\%). + +\subsection{Laboratory Data L2} + +The following code defines example dataset L2 from the FOCUS kinetics +report, p. 287 + +\begin{Schunk} +\begin{Sinput} +R> library("mkin") +R> FOCUS_2006_L2 = 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)) +R> FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2) +\end{Sinput} +\end{Schunk} + +Again, the SFO model is fitted and a summary is obtained. + +\begin{Schunk} +\begin{Sinput} +R> m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE) +R> summary(m.L2.SFO) +\end{Sinput} +\begin{Soutput} +mkin version: 0.9.10 +R version: 2.15.2 +Date of fit: Sat Feb 16 21:38:15 2013 +Date of summary: Sat Feb 16 21:38:15 2013 + +Equations: +[1] d_parent = - k_parent_sink * parent + +Starting values for optimised parameters: + initial type transformed +parent_0 100.0 state 100.000000 +k_parent_sink 0.1 deparm -2.302585 + +Fixed parameter values: +None + +Optimised, transformed parameters: + Estimate Std. Error +parent_0 91.4656 3.807 +k_parent_sink -0.4112 0.107 + +Backtransformed parameters: + Estimate +parent_0 91.466 +k_parent_sink 0.663 + +Residual standard error: 5.51 on 10 degrees of freedom + +Chi2 error levels in percent: + err.min n.optim df +All data 14.38 2 4 +parent 14.38 2 4 + +Estimated disappearance times: + DT50 DT90 +parent 1.046 3.474 + +Estimated formation fractions: + ff +parent_sink 1 + +Parameter correlation: + parent_0 k_parent_sink +parent_0 1.0000 0.4295 +k_parent_sink 0.4295 1.0000 + +Data: + time variable observed predicted residual + 0 parent 96.1 91.4656079103 4.6344 + 0 parent 91.8 91.4656079103 0.3344 + 1 parent 41.4 47.1395280371 -5.7395 + 1 parent 38.7 47.1395280371 -8.4395 + 3 parent 19.3 12.5210295280 6.7790 + 3 parent 22.3 12.5210295280 9.7790 + 7 parent 4.6 0.8833842647 3.7166 + 7 parent 4.6 0.8833842647 3.7166 + 14 parent 2.6 0.0085318162 2.5915 + 14 parent 1.2 0.0085318162 1.1915 + 28 parent 0.3 0.0000007958 0.3000 + 28 parent 0.6 0.0000007958 0.6000 +\end{Soutput} +\end{Schunk} + +The $\chi^2$ error level of 14\% suggests that the model does not fit very well. +This is also obvious from the plots of the fit and the residuals. + +\begin{Schunk} +\begin{Sinput} +R> plot(m.L2.SFO) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L2_SFO_plot} + +In the FOCUS kinetics report, it is stated that there is no apparent systematic +error observed from the residual plot up to the measured DT90 (approximately at +day 5), and there is an underestimation beyond that point. + +\begin{Schunk} +\begin{Sinput} +R> plot(m.L2.SFO$data$time, m.L2.SFO$data$residual, ++ xlab = "Time", ylab = "Residual", ylim = c(-10, 10)) +R> abline(h = 0, lty = 2) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L2_SFO_residuals} + +We may add that it is difficult to judge the random nature of the residuals just +from the three samplings at days 0, 1 and 3. Also, it is not clear why a +consistent underestimation after the approximate DT90 should be irrelevant. + +For comparison, the FOMC model is fitted as well, and the $\chi^2$ error level +is checked. + +\begin{Schunk} +\begin{Sinput} +R> m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet=TRUE) +R> plot(m.L2.FOMC) +R> s.m.L2.FOMC <- summary(m.L2.FOMC) +R> s.m.L2.FOMC$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.06204245 3 3 +parent 0.06204245 3 3 +\end{Soutput} +\end{Schunk} +\includegraphics{examples-L2_FOMC} + +The error level at which the $\chi^2$ test passes is much lower in this case. +Therefore, the FOMC model provides a better description of the data, as less +experimental error has to be assumed in order to explain the data. + +Fitting the four parameter DFOP model does not further reduce the +$\chi^2$ error level. + +\begin{Schunk} +\begin{Sinput} +R> m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet=TRUE) +R> plot(m.L2.DFOP) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L2_DFOP} + +Here, the default starting parameters for the DFOP model obviously do not lead +to a reasonable solution. Therefore the fit is repeated with different starting +parameters. + +\begin{Schunk} +\begin{Sinput} +R> m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, ++ parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8), ++ quiet=TRUE) +R> plot(m.L2.DFOP) +R> summary(m.L2.DFOP) +\end{Sinput} +\begin{Soutput} +mkin version: 0.9.10 +R version: 2.15.2 +Date of fit: Sat Feb 16 21:38:16 2013 +Date of summary: Sat Feb 16 21:38:16 2013 + +Equations: +[1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent + +Starting values for optimised parameters: + initial type transformed +parent_0 1e+02 state 100.0000000 +k1 1e+00 deparm 0.0000000 +k2 1e-02 deparm -4.6051702 +g 8e-01 deparm 0.9802581 + +Fixed parameter values: +None + +Optimised, transformed parameters: + Estimate Std. Error +parent_0 93.9500 NA +k1 4.9589 NA +k2 -1.0880 NA +g -0.2821 NA + +Backtransformed parameters: + Estimate +parent_0 93.950 +k1 142.434 +k2 0.337 +g 0.402 + +Residual standard error: 1.732 on 8 degrees of freedom + +Chi2 error levels in percent: + err.min n.optim df +All data 2.529 4 2 +parent 2.529 4 2 + +Estimated disappearance times: + DT50 DT90 +parent NA NA + +Estimated formation fractions: +[1] ff +<0 rows> (or 0-length row.names) + +Data: + time variable observed predicted residual + 0 parent 96.1 93.950000 2.1500 + 0 parent 91.8 93.950000 -2.1500 + 1 parent 41.4 40.143423 1.2566 + 1 parent 38.7 40.143423 -1.4434 + 3 parent 19.3 20.464500 -1.1645 + 3 parent 22.3 20.464500 1.8355 + 7 parent 4.6 5.318322 -0.7183 + 7 parent 4.6 5.318322 -0.7183 + 14 parent 2.6 0.503070 2.0969 + 14 parent 1.2 0.503070 0.6969 + 28 parent 0.3 0.004501 0.2955 + 28 parent 0.6 0.004501 0.5955 +\end{Soutput} +\begin{Sinput} +R> s.m.L2.DFOP <- summary(m.L2.DFOP) +R> s.m.L2.DFOP$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.02528763 4 2 +parent 0.02528763 4 2 +\end{Soutput} +\end{Schunk} +\includegraphics{examples-L2_DFOP_2} + +Therefore, the FOMC model is clearly the best-fit model based on the +$\chi^2$ error level criterion. + +\subsection{Laboratory Data L3} + +The following code defines example dataset L3 from the FOCUS kinetics +report, p. 290 + +\begin{Schunk} +\begin{Sinput} +R> library("mkin") +R> FOCUS_2006_L3 = 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_mkin <- mkin_wide_to_long(FOCUS_2006_L3) +\end{Sinput} +\end{Schunk} + +SFO model, summary and plot: + +\begin{Schunk} +\begin{Sinput} +R> m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet=TRUE) +R> summary(m.L3.SFO) +\end{Sinput} +\begin{Soutput} +mkin version: 0.9.10 +R version: 2.15.2 +Date of fit: Sat Feb 16 21:38:16 2013 +Date of summary: Sat Feb 16 21:38:16 2013 + +Equations: +[1] d_parent = - k_parent_sink * parent + +Starting values for optimised parameters: + initial type transformed +parent_0 100.0 state 100.000000 +k_parent_sink 0.1 deparm -2.302585 + +Fixed parameter values: +None + +Optimised, transformed parameters: + Estimate Std. Error +parent_0 74.873 8.458 +k_parent_sink -3.678 0.326 + +Backtransformed parameters: + Estimate +parent_0 74.873 +k_parent_sink 0.025 + +Residual standard error: 12.91 on 6 degrees of freedom + +Chi2 error levels in percent: + err.min n.optim df +All data 21.24 2 6 +parent 21.24 2 6 + +Estimated disappearance times: + DT50 DT90 +parent 27.43 91.12 + +Estimated formation fractions: + ff +parent_sink 1 + +Parameter correlation: + parent_0 k_parent_sink +parent_0 1.0000 0.5484 +k_parent_sink 0.5484 1.0000 + +Data: + time variable observed predicted residual + 0 parent 97.8 74.873 22.92734 + 3 parent 60.0 69.407 -9.40654 + 7 parent 51.0 62.734 -11.73403 + 14 parent 43.0 52.563 -9.56336 + 30 parent 35.0 35.083 -0.08281 + 60 parent 22.0 16.439 5.56137 + 91 parent 15.0 7.510 7.48961 + 120 parent 12.0 3.609 8.39083 +\end{Soutput} +\begin{Sinput} +R> plot(m.L3.SFO) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L3_SFO} + +The $\chi^2$ error level of 22\% as well as the plot suggest that the model +does not fit very well. + +The FOMC model performs better: + +\begin{Schunk} +\begin{Sinput} +R> m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet=TRUE) +R> plot(m.L3.FOMC) +R> s.m.L3.FOMC <- summary(m.L3.FOMC) +R> s.m.L3.FOMC$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.07321867 3 5 +parent 0.07321867 3 5 +\end{Soutput} +\begin{Sinput} +R> endpoints(m.L3.FOMC) +\end{Sinput} +\begin{Soutput} +$distimes + DT50 DT90 +parent 7.729478 431.2428 + +$ff +logical(0) + +$SFORB +logical(0) +\end{Soutput} +\end{Schunk} +\includegraphics{examples-L3_FOMC} + +The error level at which the $\chi^2$ test passes is 7\% in this case. + +Fitting the four parameter DFOP model further reduces the $\chi^2$ error level +considerably: + +\begin{Schunk} +\begin{Sinput} +R> m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet=TRUE) +R> plot(m.L3.DFOP) +R> s.m.L3.DFOP <- summary(m.L3.DFOP) +R> s.m.L3.DFOP$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.02223992 4 4 +parent 0.02223992 4 4 +\end{Soutput} +\end{Schunk} +\includegraphics{examples-L3_DFOP} + +Therefore, the DFOP model is the best-fit model based on the $\chi^2$ error +level criterion for laboratory data L3. + +\subsection{Laboratory Data L4} + +The following code defines example dataset L4 from the FOCUS kinetics +report, p. 293 + +\begin{Schunk} +\begin{Sinput} +R> library("mkin") +R> FOCUS_2006_L4 = 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_mkin <- mkin_wide_to_long(FOCUS_2006_L4) +\end{Sinput} +\end{Schunk} + +SFO model, summary and plot: + +\begin{Schunk} +\begin{Sinput} +R> m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet=TRUE) +R> summary(m.L4.SFO) +\end{Sinput} +\begin{Soutput} +mkin version: 0.9.10 +R version: 2.15.2 +Date of fit: Sat Feb 16 21:38:17 2013 +Date of summary: Sat Feb 16 21:38:17 2013 + +Equations: +[1] d_parent = - k_parent_sink * parent + +Starting values for optimised parameters: + initial type transformed +parent_0 100.0 state 100.000000 +k_parent_sink 0.1 deparm -2.302585 + +Fixed parameter values: +None + +Optimised, transformed parameters: + Estimate Std. Error +parent_0 96.44 1.949 +k_parent_sink -5.03 0.080 + +Backtransformed parameters: + Estimate +parent_0 96.442 +k_parent_sink 0.007 + +Residual standard error: 3.651 on 6 degrees of freedom + +Chi2 error levels in percent: + err.min n.optim df +All data 3.288 2 6 +parent 3.288 2 6 + +Estimated disappearance times: + DT50 DT90 +parent 106 352 + +Estimated formation fractions: + ff +parent_sink 1 + +Parameter correlation: + parent_0 k_parent_sink +parent_0 1.0000 0.5865 +k_parent_sink 0.5865 1.0000 + +Data: + time variable observed predicted residual + 0 parent 96.6 96.44 0.1585 + 3 parent 96.3 94.57 1.7324 + 7 parent 94.3 92.13 2.1744 + 14 parent 88.8 88.00 0.7972 + 30 parent 74.9 79.26 -4.3589 + 60 parent 59.9 65.14 -5.2376 + 91 parent 53.5 53.18 0.3167 + 120 parent 49.0 43.99 5.0054 +\end{Soutput} +\begin{Sinput} +R> plot(m.L4.SFO) +\end{Sinput} +\end{Schunk} +\includegraphics{examples-L4_SFO} + +The $\chi^2$ error level of 3.3\% as well as the plot suggest that the model +fits very well. + +The FOMC model for comparison + +\begin{Schunk} +\begin{Sinput} +R> m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet=TRUE) +R> plot(m.L4.FOMC) +R> s.m.L4.FOMC <- summary(m.L4.FOMC) +R> s.m.L4.FOMC$errmin +\end{Sinput} +\begin{Soutput} + err.min n.optim df +All data 0.02027643 3 5 +parent 0.02027643 3 5 +\end{Soutput} +\end{Schunk} +\includegraphics{examples-L4_FOMC} + +The error level at which the $\chi^2$ test passes is slightly lower for the FOMC +model. However, the difference appears negligible. + +\bibliographystyle{plainnat} +\bibliography{references} + +\end{document} +% vim: set foldmethod=syntax: diff --git a/vignettes/examples.toc b/vignettes/examples.toc new file mode 100644 index 00000000..f25aa62f --- /dev/null +++ b/vignettes/examples.toc @@ -0,0 +1,5 @@ +\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}{6}{subsection.1.2} +\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{14}{subsection.1.3} +\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{20}{subsection.1.4} |