diff options
30 files changed, 2059 insertions, 11 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 0ef8ba60..c76ca01e 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: 0.9-09 -Date: 2013-02-05 +Version: 0.9-10 +Date: 2013-02-16 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/R/mkinfit.R b/R/mkinfit.R index f574b6eb..411cb40c 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -158,7 +158,7 @@ mkinfit <- function(mkinmod, observed, points(subset(observed, name == obs_var, c(time, value)),
pch = pch_obs[obs_var], col = col_obs[obs_var])
}
- matlines(out_plot$time, out_plot[-1], co = col_obs, lty = lty_obs)
+ matlines(out_plot$time, out_plot[-1], col = col_obs, lty = lty_obs)
legend("topright", inset=c(0.05, 0.05), legend=obs_vars,
col=col_obs, pch=pch_obs, lty=1:length(pch_obs))
}
diff --git a/R/mkinresplot.R b/R/mkinresplot.R index 63927947..b3482789 100644 --- a/R/mkinresplot.R +++ b/R/mkinresplot.R @@ -19,7 +19,7 @@ # this program. If not, see <http://www.gnu.org/licenses/>
mkinresplot <- function (object, obs_vars = vector(),
- xlab = "Time [days]", ylab = "Residual [% of applied radioactivity]",
+ xlab = "Time", ylab = "Residual",
maxabs = "auto", legend= TRUE, lpos = "topright", ...)
{
obs_vars_all <- as.character(unique(object$data$variable))
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 1858aa8a..b47678ba 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -1,8 +1,8 @@ plot.mkinfit <- function(x, fit = x, xlab = "Time", ylab = "Observed", - xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), + xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)), col_obs = 1:length(fit$mkinmod$map), - pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)), + pch_obs = col_obs, lty_obs = 1, add = FALSE, legend = !add, ...) { solution_type = fit$solution_type diff --git a/man/mkin_long_to_wide.Rd b/man/mkin_long_to_wide.Rd index 6fa18606..e5836640 100644 --- a/man/mkin_long_to_wide.Rd +++ b/man/mkin_long_to_wide.Rd @@ -13,8 +13,9 @@ mkin_long_to_wide(long_data, time = "time", outtime = "time") } \arguments{ \item{long_data}{ - The dataframe must contain one variable with the time values specified by the - \code{time} argument and one column of observed values named "value". + The dataframe must contain one variable called "time" with the time values specified by the + \code{time} argument, one column called "name" with the grouping of the observed values, and + finally one column of observed values called "value". } \item{time}{ The name of the time variable in the long input data. diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 181da4bd..319b1b35 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -26,7 +26,7 @@ mkinfit(mkinmod, observed, } \item{observed}{ The observed data. It has to be in the long format as described in - \code{\link{modFit}}, i.e. the first column must contain the name of the + \code{\link{modFit}}, i.e. the first column called "name" must contain the name of the observed variable for each data point. The second column must contain the times of observation, named "time". The third column must be named "value" and contain the observed values. Optionally, a further column can contain diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index 0b48692c..8e3f18a4 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -9,7 +9,7 @@ }
\usage{
mkinresplot(object, obs_vars = vector(),
- xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]",
+ xlab = "Time", ylab = "Residual",
maxabs = "auto", legend = TRUE, lpos = "topright", ...)
}
\arguments{
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 01b8cec7..56ee551f 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -10,7 +10,7 @@ } \usage{ \method{plot}{mkinfit}(x, fit = x, xlab = "Time", ylab = "Observed", - xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), + xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)), col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, lty_obs = 1, add = FALSE, legend = !add, ...) } 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$ -- 0 +newline$ -- 24 +num.names$ -- 12 +pop$ -- 19 +preamble$ -- 1 +purify$ -- 9 +quote$ -- 0 +skip$ -- 39 +stack$ -- 0 +substring$ -- 6 +swap$ -- 7 +text.length$ -- 0 +text.prefix$ -- 0 +top$ -- 0 +type$ -- 33 +warning$ -- 0 +while$ -- 9 +width$ -- 0 +write$ -- 46 diff --git a/vignettes/examples.log b/vignettes/examples.log new file mode 100644 index 00000000..c1362041 --- /dev/null +++ b/vignettes/examples.log @@ -0,0 +1,944 @@ +This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) (format=pdflatex 2012.11.5) 16 FEB 2013 21:38 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**examples.tex +(./examples.tex +LaTeX2e <2011/06/27> +Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ng +erman, german, swissgerman, ngerman-x-2012-05-30, german-x-2012-05-30, loaded. +(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls +Document Class: article 2007/10/19 v1.4h Standard LaTeX document class +(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo +File: size12.clo 2007/10/19 v1.4h Standard LaTeX file (size option) +) +\c@part=\count79 +\c@section=\count80 +\c@subsection=\count81 +\c@subsubsection=\count82 +\c@paragraph=\count83 +\c@subparagraph=\count84 +\c@figure=\count85 +\c@table=\count86 +\abovecaptionskip=\skip41 +\belowcaptionskip=\skip42 +\bibindent=\dimen102 +) +(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty +Package: a4wide 1994/08/30 + +(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty +Package: a4 2004/04/15 v1.2g A4 based page layout +)) (./header.tex +(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty +Package: booktabs 2005/04/14 v1.61803 publication quality tables +\heavyrulewidth=\dimen103 +\lightrulewidth=\dimen104 +\cmidrulewidth=\dimen105 +\belowrulesep=\dimen106 +\belowbottomsep=\dimen107 +\aboverulesep=\dimen108 +\abovetopsep=\dimen109 +\cmidrulesep=\dimen110 +\cmidrulekern=\dimen111 +\defaultaddspace=\dimen112 +\@cmidla=\count87 +\@cmidlb=\count88 +\@aboverulesep=\dimen113 +\@belowrulesep=\dimen114 +\@thisruleclass=\count89 +\@lastruleclass=\count90 +\@thisrulewidth=\dimen115 +) +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty +Package: amsfonts 2009/06/22 v3.00 Basic AMSFonts support +\@emptytoks=\toks14 +\symAMSa=\mathgroup4 +\symAMSb=\mathgroup5 +LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold' +(Font) U/euf/m/n --> U/euf/b/n on input line 96. +) +(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty +Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols) +\symlasy=\mathgroup6 +LaTeX Font Info: Overwriting symbol font `lasy' in version `bold' +(Font) U/lasy/m/n --> U/lasy/b/n on input line 47. +) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty +Package: amsmath 2000/07/18 v2.13 AMS math features +\@mathmargin=\skip43 + +For additional information on amsmath, use the `?' option. +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty +Package: amstext 2000/06/29 v2.01 + +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty +File: amsgen.sty 1999/11/30 v2.0 +\@emptytoks=\toks15 +\ex@=\dimen116 +)) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty +Package: amsbsy 1999/11/29 v1.2d +\pmbraise@=\dimen117 +) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty +Package: amsopn 1999/12/14 v2.01 operator names +) +\inf@bad=\count91 +LaTeX Info: Redefining \frac on input line 211. +\uproot@=\count92 +\leftroot@=\count93 +LaTeX Info: Redefining \overline on input line 307. +\classnum@=\count94 +\DOTSCASE@=\count95 +LaTeX Info: Redefining \ldots on input line 379. +LaTeX Info: Redefining \dots on input line 382. +LaTeX Info: Redefining \cdots on input line 467. +\Mathstrutbox@=\box26 +\strutbox@=\box27 +\big@size=\dimen118 +LaTeX Font Info: Redeclaring font encoding OML on input line 567. +LaTeX Font Info: Redeclaring font encoding OMS on input line 568. +\macc@depth=\count96 +\c@MaxMatrixCols=\count97 +\dotsspace@=\muskip10 +\c@parentequation=\count98 +\dspbrk@lvl=\count99 +\tag@help=\toks16 +\row@=\count100 +\column@=\count101 +\maxfields@=\count102 +\andhelp@=\toks17 +\eqnshift@=\dimen119 +\alignsep@=\dimen120 +\tagshift@=\dimen121 +\tagwidth@=\dimen122 +\totwidth@=\dimen123 +\lineht@=\dimen124 +\@envbody=\toks18 +\multlinegap=\skip44 +\multlinetaggap=\skip45 +\mathdisplay@stack=\toks19 +LaTeX Info: Redefining \[ on input line 2666. +LaTeX Info: Redefining \] on input line 2667. +) +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty +Package: amssymb 2009/06/22 v3.00 +) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty +Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) + +(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty +Package: keyval 1999/03/16 v1.13 key=value parser (DPC) +\KV@toks@=\toks20 +) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty +Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR) + +(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty +Package: trig 1999/03/16 v1.09 sin cos tan (DPC) +) +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg +File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live +) +Package graphics Info: Driver file: pdftex.def on input line 91. + +(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def +File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX + +(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty +Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty +Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO) +) +\Gread@gobject=\count103 +)) +\Gin@req@height=\dimen125 +\Gin@req@width=\dimen126 +) +(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty +Package: parskip 2001/04/09 non-zero parskip adjustments +) +(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty +Package: natbib 2010/09/13 8.31b (PWD, AO) +\bibhang=\skip46 +\bibsep=\skip47 +LaTeX Info: Redefining \cite on input line 694. +\c@NAT@ctr=\count104 +) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty +Package: hyperref 2012/05/13 v6.82q Hypertext links for LaTeX + +(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty +Package: hobsub-hyperref 2012/05/28 v1.13 Bundle oberdiek, subset hyperref (HO) + + +(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty +Package: hobsub-generic 2012/05/28 v1.13 Bundle oberdiek, subset generic (HO) +Package: hobsub 2012/05/28 v1.13 Construct package bundles (HO) +Package hobsub Info: Skipping package `infwarerr' (already loaded). +Package hobsub Info: Skipping package `ltxcmds' (already loaded). +Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO) +Package ifluatex Info: LuaTeX not detected. +Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO) +Package ifvtex Info: VTeX not detected. +Package: intcalc 2007/09/27 v1.1 Expandable calculations with integers (HO) +Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO) +Package ifpdf Info: pdfTeX in PDF mode is detected. +Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO) +Package etexcmds Info: Could not find \expanded. +(etexcmds) That can mean that you are not using pdfTeX 1.50 or +(etexcmds) that some package has redefined \expanded. +(etexcmds) In the latter case, load this package earlier. +Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO) +Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO) +Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO +) +Package pdftexcmds Info: LuaTeX not detected. +Package pdftexcmds Info: \pdf@primitive is available. +Package pdftexcmds Info: \pdf@ifprimitive is available. +Package pdftexcmds Info: \pdfdraftmode found. +Package: pdfescape 2011/11/25 v1.13 Implements pdfTeX's escape features (HO) +Package: bigintcalc 2012/04/08 v1.3 Expandable calculations on big integers (HO +) +Package: bitset 2011/01/30 v1.1 Handle bit-vector datatype (HO) +Package: uniquecounter 2011/01/30 v1.2 Provide unlimited unique counter (HO) +) +Package hobsub Info: Skipping package `hobsub' (already loaded). +Package: letltxmacro 2010/09/02 v1.4 Let assignment for LaTeX macros (HO) +Package: hopatch 2012/05/28 v1.2 Wrapper for package hooks (HO) +Package: xcolor-patch 2011/01/30 xcolor patch +Package: atveryend 2011/06/30 v1.8 Hooks at the very end of document (HO) +Package atveryend Info: \enddocument detected (standard20110627). +Package: atbegshi 2011/10/05 v1.16 At begin shipout hook (HO) +Package: refcount 2011/10/16 v3.4 Data extraction from label references (HO) +Package: hycolor 2011/01/30 v1.7 Color options for hyperref/bookmark (HO) +) +(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty +Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional +) +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty +Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO) +) +\@linkdim=\dimen127 +\Hy@linkcounter=\count105 +\Hy@pagecounter=\count106 + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def +File: pd1enc.def 2012/05/13 v6.82q Hyperref: PDFDocEncoding definition (HO) +) +\Hy@SavedSpaceFactor=\count107 + +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg +File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive +) +Package hyperref Info: Hyper figures OFF on input line 4062. +Package hyperref Info: Link nesting OFF on input line 4067. +Package hyperref Info: Hyper index ON on input line 4070. +Package hyperref Info: Plain pages OFF on input line 4077. +Package hyperref Info: Backreferencing OFF on input line 4082. +Package hyperref Info: Implicit mode ON; LaTeX internals redefined. +Package hyperref Info: Bookmarks ON on input line 4300. +\c@Hy@tempcnt=\count108 + +(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty +\Urlmuskip=\muskip11 +Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc. +) +LaTeX Info: Redefining \url on input line 4653. +\Fld@menulength=\count109 +\Field@Width=\dimen128 +\Fld@charsize=\dimen129 +Package hyperref Info: Hyper figures OFF on input line 5773. +Package hyperref Info: Link nesting OFF on input line 5778. +Package hyperref Info: Hyper index ON on input line 5781. +Package hyperref Info: backreferencing OFF on input line 5788. +Package hyperref Info: Link coloring OFF on input line 5793. +Package hyperref Info: Link coloring with OCG OFF on input line 5798. +Package hyperref Info: PDF/A mode OFF on input line 5803. +LaTeX Info: Redefining \ref on input line 5843. +LaTeX Info: Redefining \pageref on input line 5847. +\Hy@abspage=\count110 +\c@Item=\count111 +\c@Hfootnote=\count112 +) + +Package hyperref Message: Driver (autodetected): hpdftex. + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def +File: hpdftex.def 2012/05/13 v6.82q Hyperref driver for pdfTeX +\Fld@listcount=\count113 +\c@bookmark@seq@number=\count114 + +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty +Package: rerunfilecheck 2011/04/15 v1.7 Rerun checks for auxiliary files (HO) +Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2 +82. +) +\Hy@SectionHShift=\skip48 +) +(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty +Package: inputenc 2008/03/30 v1.1d Input encoding file +\inpenc@prehook=\toks21 +\inpenc@posthook=\toks22 + +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def +File: utf8.def 2008/04/05 v1.1m UTF-8 support for inputenc +Now handling font encoding OML ... +... no UTF-8 mapping file for font encoding OML +Now handling font encoding T1 ... +... processing UTF-8 mapping file for font encoding T1 + +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu +File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc + defining Unicode char U+00A1 (decimal 161) + defining Unicode char U+00A3 (decimal 163) + defining Unicode char U+00AB (decimal 171) + defining Unicode char U+00BB (decimal 187) + defining Unicode char U+00BF (decimal 191) + defining Unicode char U+00C0 (decimal 192) + defining Unicode char U+00C1 (decimal 193) + defining Unicode char U+00C2 (decimal 194) + defining Unicode char U+00C3 (decimal 195) + defining Unicode char U+00C4 (decimal 196) + defining Unicode char U+00C5 (decimal 197) + defining Unicode char U+00C6 (decimal 198) + defining Unicode char U+00C7 (decimal 199) + defining Unicode char U+00C8 (decimal 200) + defining Unicode char U+00C9 (decimal 201) + defining Unicode char U+00CA (decimal 202) + defining Unicode char U+00CB (decimal 203) + defining Unicode char U+00CC (decimal 204) + defining Unicode char U+00CD (decimal 205) + defining Unicode char U+00CE (decimal 206) + defining Unicode char U+00CF (decimal 207) + defining Unicode char U+00D0 (decimal 208) + defining Unicode char U+00D1 (decimal 209) + defining Unicode char U+00D2 (decimal 210) + defining Unicode char U+00D3 (decimal 211) + defining Unicode char U+00D4 (decimal 212) + defining Unicode char U+00D5 (decimal 213) + defining Unicode char U+00D6 (decimal 214) + defining Unicode char U+00D8 (decimal 216) + defining Unicode char U+00D9 (decimal 217) + defining Unicode char U+00DA (decimal 218) + defining Unicode char U+00DB (decimal 219) + defining Unicode char U+00DC (decimal 220) + defining Unicode char U+00DD (decimal 221) + defining Unicode char U+00DE (decimal 222) + defining Unicode char U+00DF (decimal 223) + defining Unicode char U+00E0 (decimal 224) + defining Unicode char U+00E1 (decimal 225) + defining Unicode char U+00E2 (decimal 226) + defining Unicode char U+00E3 (decimal 227) + defining Unicode char U+00E4 (decimal 228) + defining Unicode char U+00E5 (decimal 229) + defining Unicode char U+00E6 (decimal 230) + defining Unicode char U+00E7 (decimal 231) + defining Unicode char U+00E8 (decimal 232) + defining Unicode char U+00E9 (decimal 233) + defining Unicode char U+00EA (decimal 234) + defining Unicode char U+00EB (decimal 235) + defining Unicode char U+00EC (decimal 236) + defining Unicode char U+00ED (decimal 237) + defining Unicode char U+00EE (decimal 238) + defining Unicode char U+00EF (decimal 239) + defining Unicode char U+00F0 (decimal 240) + defining Unicode char U+00F1 (decimal 241) + defining Unicode char U+00F2 (decimal 242) + defining Unicode char U+00F3 (decimal 243) + defining Unicode char U+00F4 (decimal 244) + defining Unicode char U+00F5 (decimal 245) + defining Unicode char U+00F6 (decimal 246) + defining Unicode char U+00F8 (decimal 248) + defining Unicode char U+00F9 (decimal 249) + defining Unicode char U+00FA (decimal 250) + defining Unicode char U+00FB (decimal 251) + defining Unicode char U+00FC (decimal 252) + defining Unicode char U+00FD (decimal 253) + defining Unicode char U+00FE (decimal 254) + defining Unicode char U+00FF (decimal 255) + defining Unicode char U+0102 (decimal 258) + defining Unicode char U+0103 (decimal 259) + defining Unicode char U+0104 (decimal 260) + defining Unicode char U+0105 (decimal 261) + defining Unicode char U+0106 (decimal 262) + defining Unicode char U+0107 (decimal 263) + defining Unicode char U+010C (decimal 268) + defining Unicode char U+010D (decimal 269) + defining Unicode char U+010E (decimal 270) + defining Unicode char U+010F (decimal 271) + defining Unicode char U+0110 (decimal 272) + defining Unicode char U+0111 (decimal 273) + defining Unicode char U+0118 (decimal 280) + defining Unicode char U+0119 (decimal 281) + defining Unicode char U+011A (decimal 282) + defining Unicode char U+011B (decimal 283) + defining Unicode char U+011E (decimal 286) + defining Unicode char U+011F (decimal 287) + defining Unicode char U+0130 (decimal 304) + defining Unicode char U+0131 (decimal 305) + defining Unicode char U+0132 (decimal 306) + defining Unicode char U+0133 (decimal 307) + defining Unicode char U+0139 (decimal 313) + defining Unicode char U+013A (decimal 314) + defining Unicode char U+013D (decimal 317) + defining Unicode char U+013E (decimal 318) + defining Unicode char U+0141 (decimal 321) + defining Unicode char U+0142 (decimal 322) + defining Unicode char U+0143 (decimal 323) + defining Unicode char U+0144 (decimal 324) + defining Unicode char U+0147 (decimal 327) + defining Unicode char U+0148 (decimal 328) + defining Unicode char U+014A (decimal 330) + defining Unicode char U+014B (decimal 331) + defining Unicode char U+0150 (decimal 336) + defining Unicode char U+0151 (decimal 337) + defining Unicode char U+0152 (decimal 338) + defining Unicode char U+0153 (decimal 339) + defining Unicode char U+0154 (decimal 340) + defining Unicode char U+0155 (decimal 341) + defining Unicode char U+0158 (decimal 344) + defining Unicode char U+0159 (decimal 345) + defining Unicode char U+015A (decimal 346) + defining Unicode char U+015B (decimal 347) + defining Unicode char U+015E (decimal 350) + defining Unicode char U+015F (decimal 351) + defining Unicode char U+0160 (decimal 352) + defining Unicode char U+0161 (decimal 353) + defining Unicode char U+0162 (decimal 354) + defining Unicode char U+0163 (decimal 355) + defining Unicode char U+0164 (decimal 356) + defining Unicode char U+0165 (decimal 357) + defining Unicode char U+016E (decimal 366) + defining Unicode char U+016F (decimal 367) + defining Unicode char U+0170 (decimal 368) + defining Unicode char U+0171 (decimal 369) + defining Unicode char U+0178 (decimal 376) + defining Unicode char U+0179 (decimal 377) + defining Unicode char U+017A (decimal 378) + defining Unicode char U+017B (decimal 379) + defining Unicode char U+017C (decimal 380) + defining Unicode char U+017D (decimal 381) + defining Unicode char U+017E (decimal 382) + defining Unicode char U+200C (decimal 8204) + defining Unicode char U+2013 (decimal 8211) + defining Unicode char U+2014 (decimal 8212) + defining Unicode char U+2018 (decimal 8216) + defining Unicode char U+2019 (decimal 8217) + defining Unicode char U+201A (decimal 8218) + defining Unicode char U+201C (decimal 8220) + defining Unicode char U+201D (decimal 8221) + defining Unicode char U+201E (decimal 8222) + defining Unicode char U+2030 (decimal 8240) + defining Unicode char U+2031 (decimal 8241) + defining Unicode char U+2039 (decimal 8249) + defining Unicode char U+203A (decimal 8250) + defining Unicode char U+2423 (decimal 9251) +) +Now handling font encoding OT1 ... +... processing UTF-8 mapping file for font encoding OT1 + +(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu +File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc + defining Unicode char U+00A1 (decimal 161) + defining Unicode char U+00A3 (decimal 163) + defining Unicode char U+00B8 (decimal 184) + defining Unicode char U+00BF (decimal 191) + defining Unicode char U+00C5 (decimal 197) + defining Unicode char U+00C6 (decimal 198) + defining Unicode char U+00D8 (decimal 216) + defining Unicode char U+00DF (decimal 223) + defining Unicode char U+00E6 (decimal 230) + defining Unicode char U+00EC (decimal 236) + defining Unicode char U+00ED (decimal 237) + defining Unicode char U+00EE (decimal 238) + defining Unicode char U+00EF (decimal 239) + defining Unicode char U+00F8 (decimal 248) + defining Unicode char U+0131 (decimal 305) + defining Unicode char U+0141 (decimal 321) + defining Unicode char U+0142 (decimal 322) + defining Unicode char U+0152 (decimal 338) + defining Unicode char U+0153 (decimal 339) + defining Unicode char U+2013 (decimal 8211) + defining Unicode char U+2014 (decimal 8212) + defining Unicode char U+2018 (decimal 8216) + defining Unicode char U+2019 (decimal 8217) + defining Unicode char U+201C (decimal 8220) + defining Unicode char U+201D (decimal 8221) +) +Now handling font encoding OMS ... +... processing UTF-8 mapping file for font encoding OMS + +(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu +File: omsenc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc + defining Unicode char U+00A7 (decimal 167) + defining Unicode char U+00B6 (decimal 182) + defining Unicode char U+00B7 (decimal 183) + defining Unicode char U+2020 (decimal 8224) + defining Unicode char U+2021 (decimal 8225) + defining Unicode char U+2022 (decimal 8226) +) +Now handling font encoding OMX ... +... no UTF-8 mapping file for font encoding OMX +Now handling font encoding U ... +... no UTF-8 mapping file for font encoding U +Now handling font encoding PD1 ... +... no UTF-8 mapping file for font encoding PD1 + defining Unicode char U+00A9 (decimal 169) + defining Unicode char U+00AA (decimal 170) + defining Unicode char U+00AE (decimal 174) + defining Unicode char U+00BA (decimal 186) + defining Unicode char U+02C6 (decimal 710) + defining Unicode char U+02DC (decimal 732) + defining Unicode char U+200C (decimal 8204) + defining Unicode char U+2026 (decimal 8230) + defining Unicode char U+2122 (decimal 8482) + defining Unicode char U+2423 (decimal 9251) +)) +(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty +Package: fontenc 2005/09/27 v1.99g Standard LaTeX package + +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def +File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file +LaTeX Font Info: Redeclaring font encoding T1 on input line 43. +)) +(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty +Package: ae 2001/02/12 1.3 Almost European Computer Modern + +(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty +Package: fontenc 2005/09/27 v1.99g Standard LaTeX package + +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def +File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file +LaTeX Font Info: Redeclaring font encoding T1 on input line 43. +) +LaTeX Font Info: Try loading font information for T1+aer on input line 100. + +(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd +File: t1aer.fd 1997/11/16 Font definitions for T1/aer. +))) +(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty +Package: fancyvrb 2008/02/07 + +Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix +<2008/02/07> (tvz) +\FV@CodeLineNo=\count115 +\FV@InFile=\read1 +\FV@TabBox=\box28 +\c@FancyVerbLine=\count116 +\FV@StepNumber=\count117 +\FV@OutFile=\write3 +) (/usr/share/texmf/tex/latex/R/tex/latex/upquote.sty +Package: upquote 2003/08/11 v1.1 Covington's upright-quote modification to verb +atim and verb + +(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty +Package: textcomp 2005/09/27 v1.99g Standard LaTeX package +Package textcomp Info: Sub-encoding information: +(textcomp) 5 = only ISO-Adobe without \textcurrency +(textcomp) 4 = 5 + \texteuro +(textcomp) 3 = 4 + \textohm +(textcomp) 2 = 3 + \textestimated + \textcurrency +(textcomp) 1 = TS1 - \textcircled - \t +(textcomp) 0 = TS1 (full) +(textcomp) Font families with sub-encoding setting implement +(textcomp) only a restricted character set as indicated. +(textcomp) Family '?' is the default used for unknown fonts. +(textcomp) See the documentation for details. +Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71. + +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def +File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file +Now handling font encoding TS1 ... +... processing UTF-8 mapping file for font encoding TS1 + +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu +File: ts1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc + defining Unicode char U+00A2 (decimal 162) + defining Unicode char U+00A3 (decimal 163) + defining Unicode char U+00A4 (decimal 164) + defining Unicode char U+00A5 (decimal 165) + defining Unicode char U+00A6 (decimal 166) + defining Unicode char U+00A7 (decimal 167) + defining Unicode char U+00A8 (decimal 168) + defining Unicode char U+00A9 (decimal 169) + defining Unicode char U+00AA (decimal 170) + defining Unicode char U+00AC (decimal 172) + defining Unicode char U+00AE (decimal 174) + defining Unicode char U+00AF (decimal 175) + defining Unicode char U+00B0 (decimal 176) + defining Unicode char U+00B1 (decimal 177) + defining Unicode char U+00B2 (decimal 178) + defining Unicode char U+00B3 (decimal 179) + defining Unicode char U+00B4 (decimal 180) + defining Unicode char U+00B5 (decimal 181) + defining Unicode char U+00B6 (decimal 182) + defining Unicode char U+00B7 (decimal 183) + defining Unicode char U+00B9 (decimal 185) + defining Unicode char U+00BA (decimal 186) + defining Unicode char U+00BC (decimal 188) + defining Unicode char U+00BD (decimal 189) + defining Unicode char U+00BE (decimal 190) + defining Unicode char U+00D7 (decimal 215) + defining Unicode char U+00F7 (decimal 247) + defining Unicode char U+0192 (decimal 402) + defining Unicode char U+02C7 (decimal 711) + defining Unicode char U+02D8 (decimal 728) + defining Unicode char U+02DD (decimal 733) + defining Unicode char U+0E3F (decimal 3647) + defining Unicode char U+2016 (decimal 8214) + defining Unicode char U+2020 (decimal 8224) + defining Unicode char U+2021 (decimal 8225) + defining Unicode char U+2022 (decimal 8226) + defining Unicode char U+2030 (decimal 8240) + defining Unicode char U+2031 (decimal 8241) + defining Unicode char U+203B (decimal 8251) + defining Unicode char U+203D (decimal 8253) + defining Unicode char U+2044 (decimal 8260) + defining Unicode char U+204E (decimal 8270) + defining Unicode char U+2052 (decimal 8274) + defining Unicode char U+20A1 (decimal 8353) + defining Unicode char U+20A4 (decimal 8356) + defining Unicode char U+20A6 (decimal 8358) + defining Unicode char U+20A9 (decimal 8361) + defining Unicode char U+20AB (decimal 8363) + defining Unicode char U+20AC (decimal 8364) + defining Unicode char U+20B1 (decimal 8369) + defining Unicode char U+2103 (decimal 8451) + defining Unicode char U+2116 (decimal 8470) + defining Unicode char U+2117 (decimal 8471) + defining Unicode char U+211E (decimal 8478) + defining Unicode char U+2120 (decimal 8480) + defining Unicode char U+2122 (decimal 8482) + defining Unicode char U+2126 (decimal 8486) + defining Unicode char U+2127 (decimal 8487) + defining Unicode char U+212E (decimal 8494) + defining Unicode char U+2190 (decimal 8592) + defining Unicode char U+2191 (decimal 8593) + defining Unicode char U+2192 (decimal 8594) + defining Unicode char U+2193 (decimal 8595) + defining Unicode char U+2329 (decimal 9001) + defining Unicode char U+232A (decimal 9002) + defining Unicode char U+2422 (decimal 9250) + defining Unicode char U+25E6 (decimal 9702) + defining Unicode char U+25EF (decimal 9711) + defining Unicode char U+266A (decimal 9834) +)) +LaTeX Info: Redefining \oldstylenums on input line 266. +Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281. +Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282. +Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283. +Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284. +Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285. +Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286. +Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287. +Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288. +Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289. +Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290. +Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291. +Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292. +Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293. +Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294. +Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295. +Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296. +Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297. +Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298. +Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299. +Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300. +Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301. +Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302. +Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303. +Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304. + +Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305. +Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306. +Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307. +Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308. +Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309. +Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310. +Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 311. +Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 312. +Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 313. +Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 314. +Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 315. +Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 316. +Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 317. +Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 318. +Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 319. +Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 320. +Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 321. +Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 322. +Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 323. +Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 324. +Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 325. +Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 326. +Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 327. +Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 328. +Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 329. +Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 330. +Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 331. +Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 332. +Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 333. +Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 334. +Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 335. +Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 336. +Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 337. +Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 338. +Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 339. +Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 340. +)) +(/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty +Package: relsize 2011/09/21 ver 4.0 + +Examine \normalsize starts \@setfontsize size may be \@xiipt. +Examine \small starts \@setfontsize size may be \@xipt. +Examine \footnotesize starts \@setfontsize size may be \@xpt. +Examine \large starts \@setfontsize size may be \@xivpt. +Examine \Large starts \@setfontsize size may be \@xviipt. +Examine \LARGE starts \@setfontsize size may be \@xxpt. +Examine \scriptsize starts \@setfontsize size may be \@viiipt. +Examine \tiny starts \@setfontsize size may be \@vipt. +Examine \huge starts \@setfontsize size may be \@xxvpt. +Examine \Huge starts \@setfontsize size may be \@xxvpt. )) +Package hyperref Info: Option `colorlinks' set `true' on input line 19. + + +Package hyperref Warning: Option `hyperindex' has already been used, +(hyperref) setting the option has no effect on input line 19. + +Package hyperref Info: Option `linktocpage' set `true' on input line 19. +(./examples.aux) +\openout1 = `examples.aux'. + +LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 21. +LaTeX Font Info: ... okay on input line 21. +LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 21. +LaTeX Font Info: Try loading font information for TS1+cmr on input line 21. + (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd +File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions +) +LaTeX Font Info: ... okay on input line 21. + +(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii +[Loading MPS to PDF converter (version 2006.09.02).] +\scratchcounter=\count118 +\scratchdimen=\dimen130 +\scratchbox=\box29 +\nofMPsegments=\count119 +\nofMParguments=\count120 +\everyMPshowfont=\toks23 +\MPscratchCnt=\count121 +\MPscratchDim=\dimen131 +\MPnumerator=\count122 +\makeMPintoPDFobject=\count123 +\everyMPtoPDFconversion=\toks24 +) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty +Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf + +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty +Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO) +) +Package grfext Info: Graphics extension search list: +(grfext) [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE +G,.JBIG2,.JB2,.eps] +(grfext) \AppendGraphicsExtensions on input line 452. + +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg +File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv +e +)) +\AtBeginShipoutBox=\box30 + +(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty +Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC) + +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg +File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive +) +Package color Info: Driver file: pdftex.def on input line 130. +) +Package hyperref Info: Link coloring ON on input line 21. + +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty +Package: nameref 2010/04/30 v2.40 Cross-referencing by name of section + +(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty +Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO) +) +\c@section@level=\count124 +) +LaTeX Info: Redefining \ref on input line 21. +LaTeX Info: Redefining \pageref on input line 21. +LaTeX Info: Redefining \nameref on input line 21. + +(./examples.out) (./examples.out) +\@outlinefile=\write4 +\openout4 = `examples.out'. + +LaTeX Font Info: Try loading font information for U+msa on input line 31. + +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd +File: umsa.fd 2009/06/22 v3.00 AMS symbols A +) +LaTeX Font Info: Try loading font information for U+msb on input line 31. + +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd +File: umsb.fd 2009/06/22 v3.00 AMS symbols B +) +LaTeX Font Info: Try loading font information for U+lasy on input line 31. + +(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd +File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions +) [0 + +{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./examples.toc) +\tf@toc=\write5 +\openout5 = `examples.toc'. + +LaTeX Font Info: Try loading font information for T1+aett on input line 57. + +(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd +File: t1aett.fd 1997/11/16 Font definitions for T1/aett. +) [1 + +] +LaTeX Font Info: Try loading font information for T1+pcr on input line 94. + +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd +File: t1pcr.fd 2001/06/04 font definitions for T1/pcr. +) +LaTeX Font Info: Font shape `T1/pcr/m/it' in size <10> not available +(Font) Font shape `T1/pcr/m/sl' tried instead on input line 94. + [2] +<examples-L1_SFO_plot.pdf, id=58, 433.62pt x 433.62pt> +File: examples-L1_SFO_plot.pdf Graphic file (type pdf) + +<use examples-L1_SFO_plot.pdf> +Package pdftex.def Info: examples-L1_SFO_plot.pdf used on input line 171. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [3] +<examples-L1_SFO_residuals.pdf, id=63, 433.62pt x 433.62pt> +File: examples-L1_SFO_residuals.pdf Graphic file (type pdf) + +<use examples-L1_SFO_residuals.pdf> +Package pdftex.def Info: examples-L1_SFO_residuals.pdf used on input line 184. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [4 <./examples-L1_SFO_plot.pdf>] [5 <./examples-L1_SFO_residuals.pdf>] [6] +<examples-L2_SFO_plot.pdf, id=91, 433.62pt x 433.62pt> +File: examples-L2_SFO_plot.pdf Graphic file (type pdf) + +<use examples-L2_SFO_plot.pdf> +Package pdftex.def Info: examples-L2_SFO_plot.pdf used on input line 302. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [7] +<examples-L2_SFO_residuals.pdf, id=96, 433.62pt x 433.62pt> +File: examples-L2_SFO_residuals.pdf Graphic file (type pdf) + +<use examples-L2_SFO_residuals.pdf> +Package pdftex.def Info: examples-L2_SFO_residuals.pdf used on input line 315. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [8 <./examples-L2_SFO_plot.pdf>] +<examples-L2_FOMC.pdf, id=107, 433.62pt x 433.62pt> +File: examples-L2_FOMC.pdf Graphic file (type pdf) + <use examples-L2_FOMC.pdf> +Package pdftex.def Info: examples-L2_FOMC.pdf used on input line 337. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[9 <./examples-L2_SFO_residuals.pdf>] +<examples-L2_DFOP.pdf, id=118, 433.62pt x 433.62pt> +File: examples-L2_DFOP.pdf Graphic file (type pdf) + <use examples-L2_DFOP.pdf> +Package pdftex.def Info: examples-L2_DFOP.pdf used on input line 352. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[10 <./examples-L2_FOMC.pdf>] [11 <./examples-L2_DFOP.pdf>] [12] +<examples-L2_DFOP_2.pdf, id=144, 433.62pt x 433.62pt> +File: examples-L2_DFOP_2.pdf Graphic file (type pdf) + +<use examples-L2_DFOP_2.pdf> +Package pdftex.def Info: examples-L2_DFOP_2.pdf used on input line 439. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [13] [14 <./examples-L2_DFOP_2.pdf>] [15] +<examples-L3_SFO.pdf, id=164, 433.62pt x 433.62pt> +File: examples-L3_SFO.pdf Graphic file (type pdf) + <use examples-L3_SFO.pdf> +Package pdftex.def Info: examples-L3_SFO.pdf used on input line 528. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[16] [17 <./examples-L3_SFO.pdf>] +<examples-L3_FOMC.pdf, id=179, 433.62pt x 433.62pt> +File: examples-L3_FOMC.pdf Graphic file (type pdf) + <use examples-L3_FOMC.pdf> +Package pdftex.def Info: examples-L3_FOMC.pdf used on input line 562. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[18 <./examples-L3_FOMC.pdf>] +<examples-L3_DFOP.pdf, id=191, 433.62pt x 433.62pt> +File: examples-L3_DFOP.pdf Graphic file (type pdf) + <use examples-L3_DFOP.pdf> +Package pdftex.def Info: examples-L3_DFOP.pdf used on input line 582. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[19 <./examples-L3_DFOP.pdf>] [20] +<examples-L4_SFO.pdf, id=206, 433.62pt x 433.62pt> +File: examples-L4_SFO.pdf Graphic file (type pdf) + <use examples-L4_SFO.pdf> +Package pdftex.def Info: examples-L4_SFO.pdf used on input line 671. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + +[21] <examples-L4_FOMC.pdf, id=211, 433.62pt x 433.62pt> +File: examples-L4_FOMC.pdf Graphic file (type pdf) + +<use examples-L4_FOMC.pdf> +Package pdftex.def Info: examples-L4_FOMC.pdf used on input line 691. +(pdftex.def) Requested size: 433.61894pt x 433.61894pt. + [22 <./examples-L4_SFO.pdf>] (./examples.bbl +[23 <./examples-L4_FOMC.pdf>]) +Package atveryend Info: Empty hook `BeforeClearDocument' on input line 699. + [24] +Package atveryend Info: Empty hook `AfterLastShipout' on input line 699. + (./examples.aux) +Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 699. +Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 699. +Package rerunfilecheck Info: File `examples.out' has not changed. +(rerunfilecheck) Checksum: 3F5170E33F755296C8437680AEA1EFF7;343. +Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 699. + ) +Here is how much of TeX's memory you used: + 7873 strings out of 495007 + 111249 string characters out of 3179690 + 187564 words of memory out of 3000000 + 10839 multiletter control sequences out of 15000+200000 + 38268 words of font info for 93 fonts, out of 3000000 for 9000 + 14 hyphenation exceptions out of 8191 + 31i,6n,28p,255b,512s stack positions out of 5000i,500n,10000p,200000b,50000s +{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texliv +e/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf +-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/ +fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/ +type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/p +ublic/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a +msfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ +cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmt +t12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> +Output written on examples.pdf (25 pages, 184683 bytes). +PDF statistics: + 283 PDF objects out of 1000 (max. 8388607) + 220 compressed objects within 3 object streams + 36 named destinations out of 1000 (max. 500000) + 101 words of extra memory for PDF output out of 10000 (max. 10000000) + diff --git a/vignettes/examples.out b/vignettes/examples.out new file mode 100644 index 00000000..0ccdd62b --- /dev/null +++ b/vignettes/examples.out @@ -0,0 +1,5 @@ +\BOOKMARK [1][-]{section.1}{Kinetic evaluations for parent compounds}{}% 1 +\BOOKMARK [2][-]{subsection.1.1}{Laboratory Data 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} |