summaryrefslogtreecommitdiff
path: root/vignettes
diff options
context:
space:
mode:
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/examples-FOCUS_2006_L3_2.pdfbin6609 -> 0 bytes
-rw-r--r--vignettes/examples-FOCUS_2006_L4.pdfbin6557 -> 0 bytes
-rw-r--r--vignettes/examples-L1_SFO_plot.pdfbin5572 -> 0 bytes
-rw-r--r--vignettes/examples-L1_SFO_residuals.pdfbin4718 -> 0 bytes
-rw-r--r--vignettes/examples-L2_plot.pdfbin5846 -> 0 bytes
-rw-r--r--vignettes/examples-L2_resplot.pdfbin4988 -> 0 bytes
-rw-r--r--vignettes/examples.aux29
-rw-r--r--vignettes/examples.bbl30
-rw-r--r--vignettes/examples.blg46
-rw-r--r--vignettes/examples.log617
-rw-r--r--vignettes/examples.out5
-rw-r--r--vignettes/examples.pdfbin155612 -> 155610 bytes
-rw-r--r--vignettes/examples.tex657
-rw-r--r--vignettes/examples.toc5
-rw-r--r--vignettes/kinfit.pdfbin265975 -> 227085 bytes
15 files changed, 0 insertions, 1389 deletions
diff --git a/vignettes/examples-FOCUS_2006_L3_2.pdf b/vignettes/examples-FOCUS_2006_L3_2.pdf
deleted file mode 100644
index 84272c4..0000000
--- a/vignettes/examples-FOCUS_2006_L3_2.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples-FOCUS_2006_L4.pdf b/vignettes/examples-FOCUS_2006_L4.pdf
deleted file mode 100644
index bd67e70..0000000
--- a/vignettes/examples-FOCUS_2006_L4.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples-L1_SFO_plot.pdf b/vignettes/examples-L1_SFO_plot.pdf
deleted file mode 100644
index c44f903..0000000
--- a/vignettes/examples-L1_SFO_plot.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples-L1_SFO_residuals.pdf b/vignettes/examples-L1_SFO_residuals.pdf
deleted file mode 100644
index 66cc0a0..0000000
--- a/vignettes/examples-L1_SFO_residuals.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples-L2_plot.pdf b/vignettes/examples-L2_plot.pdf
deleted file mode 100644
index d502cda..0000000
--- a/vignettes/examples-L2_plot.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples-L2_resplot.pdf b/vignettes/examples-L2_resplot.pdf
deleted file mode 100644
index 44a679e..0000000
--- a/vignettes/examples-L2_resplot.pdf
+++ /dev/null
Binary files differ
diff --git a/vignettes/examples.aux b/vignettes/examples.aux
deleted file mode 100644
index b87a0c2..0000000
--- a/vignettes/examples.aux
+++ /dev/null
@@ -1,29 +0,0 @@
-\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:mkin}
-\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}{5}{subsection.1.2}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{10}{subsection.1.3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{14}{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:mkin}{{3}{2013}{{mkin}}{{}}}
diff --git a/vignettes/examples.bbl b/vignettes/examples.bbl
deleted file mode 100644
index 29159ac..0000000
--- a/vignettes/examples.bbl
+++ /dev/null
@@ -1,30 +0,0 @@
-\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[mkin(2013)]{pkg:mkin}
-mkin.
-\newblock \emph{mkin: {R}outines for fitting kinetic models with one or more
- state variables to chemical degradation data}, 2013.
-\newblock URL \url{http://CRAN.R-project.org}.
-\newblock R package version 0.9-11.
-
-\end{thebibliography}
diff --git a/vignettes/examples.blg b/vignettes/examples.blg
deleted file mode 100644
index bbb3b5c..0000000
--- a/vignettes/examples.blg
+++ /dev/null
@@ -1,46 +0,0 @@
-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,
- 610 strings with 5517 characters,
-and the built_in function-call counts, 904 in all, are:
-= -- 84
-> -- 30
-< -- 3
-+ -- 12
-- -- 9
-* -- 57
-:= -- 153
-add.period$ -- 11
-call.type$ -- 3
-change.case$ -- 10
-chr.to.int$ -- 3
-cite$ -- 6
-duplicate$ -- 51
-empty$ -- 76
-format.name$ -- 12
-if$ -- 175
-int.to.chr$ -- 1
-int.to.str$ -- 1
-missing$ -- 0
-newline$ -- 25
-num.names$ -- 12
-pop$ -- 18
-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$ -- 48
diff --git a/vignettes/examples.log b/vignettes/examples.log
deleted file mode 100644
index 727935a..0000000
--- a/vignettes/examples.log
+++ /dev/null
@@ -1,617 +0,0 @@
-This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) (format=pdflatex 2012.11.5) 17 FEB 2013 21:08
-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/latin1.def
-File: latin1.def 2008/03/30 v1.1d Input encoding file
-))
-(/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
-)
-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 18.
-
-
-Package hyperref Warning: Option `hyperindex' has already been used,
-(hyperref) setting the option has no effect on input line 18.
-
-Package hyperref Info: Option `linktocpage' set `true' on input line 18.
-(./examples.aux)
-\openout1 = `examples.aux'.
-
-LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 20.
-LaTeX Font Info: ... okay on input line 20.
-LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 20.
-LaTeX Font Info: Try loading font information for TS1+cmr on input line 20.
- (/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 20.
-
-(/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 20.
-
-(/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 20.
-LaTeX Info: Redefining \pageref on input line 20.
-LaTeX Info: Redefining \nameref on input line 20.
-
-(./examples.out) (./examples.out)
-\@outlinefile=\write4
-\openout4 = `examples.out'.
-
-LaTeX Font Info: Try loading font information for U+msa on input line 30.
-
-(/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 30.
-
-(/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 30.
-
-(/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 55.
-
-(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd
-File: t1aett.fd 1997/11/16 Font definitions for T1/aett.
-)
-LaTeX Font Info: Try loading font information for T1+pcr on input line 77.
-
-(/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 77.
- [1
-
-] [2] [3]
-<examples-L1_SFO_plot.pdf, id=62, 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 203.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
-
-<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 212.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
- [4 <./examples-L1_SFO_plot.pdf>] [5 <./examples-L1_SFO_residuals.pdf>] [6] [7]
-
-<examples-L2_plot.pdf, id=93, 433.62pt x 433.62pt>
-File: examples-L2_plot.pdf Graphic file (type pdf)
- <use examples-L2_plot.pdf>
-Package pdftex.def Info: examples-L2_plot.pdf used on input line 384.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
-
-[8] <examples-L2_resplot.pdf, id=100, 433.62pt x 433.62pt>
-File: examples-L2_resplot.pdf Graphic file (type pdf)
-
-<use examples-L2_resplot.pdf>
-Package pdftex.def Info: examples-L2_resplot.pdf used on input line 395.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
- [9 <./examples-L2_plot.pdf>] [10 <./examples-L2_resplot.pdf>] [11] [12]
-<examples-FOCUS_2006_L3_2.pdf, id=130, 433.62pt x 433.62pt>
-File: examples-FOCUS_2006_L3_2.pdf Graphic file (type pdf)
-
-<use examples-FOCUS_2006_L3_2.pdf>
-Package pdftex.def Info: examples-FOCUS_2006_L3_2.pdf used on input line 552.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
- [13] [14 <./examples-FOCUS_2006_L3_2.pdf>]
-[15] <examples-FOCUS_2006_L4.pdf, id=150, 433.62pt x 433.62pt>
-File: examples-FOCUS_2006_L4.pdf Graphic file (type pdf)
-
-<use examples-FOCUS_2006_L4.pdf>
-Package pdftex.def Info: examples-FOCUS_2006_L4.pdf used on input line 646.
-(pdftex.def) Requested size: 433.61894pt x 433.61894pt.
- [16] (./examples.bbl [17 <./examples-FOCUS_2006_L4.pdf>])
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 656.
- [18]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 656.
- (./examples.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 656.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 656.
-Package rerunfilecheck Info: File `examples.out' has not changed.
-(rerunfilecheck) Checksum: 3F5170E33F755296C8437680AEA1EFF7;343.
-Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 656.
- )
-Here is how much of TeX's memory you used:
- 7604 strings out of 495007
- 108826 string characters out of 3179690
- 184606 words of memory out of 3000000
- 10593 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,514s 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 (19 pages, 155612 bytes).
-PDF statistics:
- 214 PDF objects out of 1000 (max. 8388607)
- 170 compressed objects within 2 object streams
- 30 named destinations out of 1000 (max. 500000)
- 71 words of extra memory for PDF output out of 10000 (max. 10000000)
-
diff --git a/vignettes/examples.out b/vignettes/examples.out
deleted file mode 100644
index 0ccdd62..0000000
--- a/vignettes/examples.out
+++ /dev/null
@@ -1,5 +0,0 @@
-\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
index 8bc6495..461d2d5 100644
--- a/vignettes/examples.pdf
+++ b/vignettes/examples.pdf
Binary files differ
diff --git a/vignettes/examples.tex b/vignettes/examples.tex
deleted file mode 100644
index 4d92a06..0000000
--- a/vignettes/examples.tex
+++ /dev/null
@@ -1,657 +0,0 @@
-% $Id: $
-%%\VignetteIndexEntry{Examples for kinetic evaluations using kinfit}
-%%\usepackage{Sweave}
-\documentclass[12pt,a4paper]{article}
-\usepackage{a4wide}
-%%\usepackage[lists,heads]{endfloat}
-\input{header}
-\hypersetup{
- pdftitle = {Examples for kinetic evaluations using kinfit},
- 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 kinfit}
-\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{mkin} package \citep{pkg:mkin}. The datasets are from Appendix 3,
-of the FOCUS kinetics report \citep{FOCUS2006, FOCUSkinetics2011}.
-
-\subsection{Laboratory Data L1}
-
-The following code defines an object containing the example dataset L1 from the
-FOCUS kinetics report, p. 284
-
-\begin{Schunk}
-\begin{Sinput}
-R> library("kinfit")
-R> FOCUS_2006_L1 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L1$data = data.frame(
-+ t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
-+ parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
-+ 72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
-+ 27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
-\end{Sinput}
-\end{Schunk}
-
-The following two lines fit the model and produce the summary report
-of the model fit. This covers the numerical analyses given in the
-FOCUS report.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits)
-R> kinreport(FOCUS_2006_L1)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:07:59 2013
-
-Data:
- t parent
-1 0 88.3
-2 0 91.4
-3 1 85.6
-4 1 84.5
-5 2 78.9
-6 2 77.6
-7 3 72.0
-8 3 71.9
-9 5 50.3
-10 5 59.4
-11 7 47.0
-12 7 45.1
-13 14 27.7
-14 14 27.3
-15 21 10.0
-16 21 10.4
-17 30 2.9
-18 30 4.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 92.4710 1.36830 67.6 0.00e+00
-k 0.0956 0.00388 24.6 1.87e-14
-
-Chi2 error estimation: 3.42 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 7.2 24.1
-\end{Soutput}
-\end{Schunk}
-
-Obviously, the FOMC model and the DFOP model were not fitted. As discussed in the
-kinfit vignette of this package, this occurs when the SFO model fits very well.
-
-We can try to force the FOMC fit using the parameters obtained using mkin.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L1$fits <- kinfit(FOCUS_2006_L1$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.FOMC = list(parent.0 = 92.47, alpha = 1.35e11, beta = 1.41e12))
-R> FOCUS_2006_L1$results <- kinresults(FOCUS_2006_L1$fits)
-R> kinreport(FOCUS_2006_L1)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 88.3
-2 0 91.4
-3 1 85.6
-4 1 84.5
-5 2 78.9
-6 2 77.6
-7 3 72.0
-8 3 71.9
-9 5 50.3
-10 5 59.4
-11 7 47.0
-12 7 45.1
-13 14 27.7
-14 14 27.3
-15 21 10.0
-16 21 10.4
-17 30 2.9
-18 30 4.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 92.4710 1.36830 67.6 0.00e+00
-k 0.0956 0.00388 24.6 1.87e-14
-
-Chi2 error estimation: 3.42 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 7.2 24.1
-\end{Soutput}
-\end{Schunk}
-
-It still does not converge. As discussed in the kinfit vignette, the FOMC model usually
-is not returned by kinfit when the SFO model fits very well. This should be seen as
-a feature, not a bug, as the FOMC model is ill-defined in such cases.
-
-A plot of the fit is obtained with the kinplot function.
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L1, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L1_SFO_plot}
-
-The residual plot can be easily obtained by
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinresplot(FOCUS_2006_L1, "SFO", ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L1_SFO_residuals}
-
-\subsection{Laboratory Data L2}
-
-The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L2$data = 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))
-\end{Sinput}
-\end{Schunk}
-
-Again, the SFO, FOMC and DFOP models are fitted and a report is printed.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits)
-R> kinreport(FOCUS_2006_L2)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.1
-2 0 91.8
-3 1 41.4
-4 1 38.7
-5 3 19.3
-6 3 22.3
-7 7 4.6
-8 7 4.6
-9 14 2.6
-10 14 1.2
-11 28 0.3
-12 28 0.6
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 91.466 3.8065 24.03 1.77e-10
-k 0.663 0.0712 9.31 1.52e-06
-
-Chi2 error estimation: 14.38 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 93.77 1.856 50.51 1.17e-12
-alpha 1.37 0.257 5.36 2.30e-04
-beta 1.23 0.363 3.40 3.95e-03
-
-Chi2 error estimation: 6.2 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 1.0 3.5
-FOMC 0.8 5.4
-\end{Soutput}
-\end{Schunk}
-
-Here, only the DFOP did not converge using default parameters. The DFOP fit can be
-obtained using refined starting parameters:
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L2$fits <- kinfit(FOCUS_2006_L2$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.DFOP = list(parent.0 = 94, g = 0.4, k1 = 142, k2 = 0.34))
-R> FOCUS_2006_L2$results <- kinresults(FOCUS_2006_L2$fits)
-R> kinreport(FOCUS_2006_L2)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.1
-2 0 91.8
-3 1 41.4
-4 1 38.7
-5 3 19.3
-6 3 22.3
-7 7 4.6
-8 7 4.6
-9 14 2.6
-10 14 1.2
-11 28 0.3
-12 28 0.6
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 91.466 3.8065 24.03 1.77e-10
-k 0.663 0.0712 9.31 1.52e-06
-
-Chi2 error estimation: 14.38 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 93.77 1.856 50.51 1.17e-12
-alpha 1.37 0.257 5.36 2.30e-04
-beta 1.23 0.363 3.40 3.95e-03
-
-Chi2 error estimation: 6.2 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 1.0 3.5
-FOMC 0.8 5.4
-\end{Soutput}
-\end{Schunk}
-
-Again, even with starting parameters very close to the optimum obtained using mkin,
-there is no convergence with kinfit. However, when looking at the fit obtained using
-mkin plotted in the mkin vignette, it is clear that the point where the break point
-of the curve, caused by the large difference between k1 and k2, is not clearly defined
-by the data. Therefore, it should be seen as a desirable feature of the
-underlying nls() function that no solution is returned.
-
-Comparison of $\chi^2$ error levels of the two models shows that the FOMC model allows
-for a better representation of the data. This is also obvious from the plot
-of the fits.
-
-\begin{Schunk}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L2, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L2_plot}
-
-Residual plots are obtained using kinresplot.
-
-\begin{Schunk}
-\begin{Sinput}
-R> par(mfrow=c(2,1))
-R> kinresplot(FOCUS_2006_L2, "SFO", ylab = "Observed")
-R> kinresplot(FOCUS_2006_L2, "FOMC", ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-L2_resplot}
-
-\subsection{Laboratory Data L3}
-
-The following code defines example dataset L3 from the FOCUS kinetics
-report, p. 290 and attempts to fit the SFO, FOMC and DFOP models.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L3 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L3$data = data.frame(
-+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
-+ parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits)
-R> kinreport(FOCUS_2006_L3)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 97.8
-2 3 60.0
-3 7 51.0
-4 14 43.0
-5 30 35.0
-6 60 22.0
-7 91 15.0
-8 120 12.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 74.8718 8.45736 8.85 5.78e-05
-k 0.0253 0.00824 3.07 1.10e-02
-
-Chi2 error estimation: 21.24 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 97.7460 1.438160 68.0 1.40e-07
-k1 0.5162 0.068841 7.5 8.46e-04
-k2 0.0138 0.000812 16.9 3.56e-05
-g 0.4566 0.017970 25.4 7.12e-06
-
-Chi2 error estimation: 2.22 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 27.4 91.1
-DFOP 7.5 123.0
-\end{Soutput}
-\end{Schunk}
-
-In this case, the FOMC model does not return a solution using kinfit. Trying with
-closer starting parameters gives success this time.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L3$fits <- kinfit(FOCUS_2006_L3$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"),
-+ start.FOMC = list(parent.0 = 100, alpha = 0.5, beta = 2))
-R> FOCUS_2006_L3$results <- kinresults(FOCUS_2006_L3$fits)
-R> kinreport(FOCUS_2006_L3)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 97.8
-2 3 60.0
-3 7 51.0
-4 14 43.0
-5 30 35.0
-6 60 22.0
-7 91 15.0
-8 120 12.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 74.8718 8.45736 8.85 5.78e-05
-k 0.0253 0.00824 3.07 1.10e-02
-
-Chi2 error estimation: 21.24 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 96.974 4.550 21.31 2.11e-06
-alpha 0.422 0.072 5.87 1.02e-03
-beta 1.858 0.881 2.11 4.44e-02
-
-Chi2 error estimation: 7.32 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 97.7460 1.438160 68.0 1.40e-07
-k1 0.5162 0.068841 7.5 8.46e-04
-k2 0.0138 0.000812 16.9 3.56e-05
-g 0.4566 0.017970 25.4 7.12e-06
-
-Chi2 error estimation: 2.22 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 27.4 91.1
-FOMC 7.7 431.2
-DFOP 7.5 123.0
-\end{Soutput}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L3, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-FOCUS_2006_L3_2}
-
-Based on the $\chi^2$ error level criterion and the visual analysis of the
-fits, the DFOP model would be the best-fit model of choice for laboratory data
-L3.
-
-\subsection{Laboratory Data L4}
-
-The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293 and attempts to fit the SFO, FOMC and DFOP models.
-
-\begin{Schunk}
-\begin{Sinput}
-R> FOCUS_2006_L4 = kinobject("Parent", "Degradation data", "")
-R> FOCUS_2006_L4$data = data.frame(
-+ t = c(0, 3, 7, 14, 30, 60, 91, 120),
-+ parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-R> FOCUS_2006_L4$fits <- kinfit(FOCUS_2006_L4$data,
-+ kinmodels = c("SFO", "FOMC", "DFOP"))
-R> FOCUS_2006_L4$results <- kinresults(FOCUS_2006_L4$fits)
-R> kinreport(FOCUS_2006_L4)
-\end{Sinput}
-\begin{Soutput}
-Parent compound: Parent
-Study type: Degradation data
-System:
-kinfit version: 1.1.10
-R version: 2.15.2
-Report generated: Sun Feb 17 21:08:00 2013
-
-Data:
- t parent
-1 0 96.6
-2 3 96.3
-3 7 94.3
-4 14 88.8
-5 30 74.9
-6 60 59.9
-7 91 53.5
-8 120 49.0
-
-
-
----
-Nonlinear least squares fit of the SFO model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 96.44152 1.948781 49.5 2.28e-09
-k 0.00654 0.000523 12.5 8.01e-06
-
-Chi2 error estimation: 3.29 %
-
-
-
----
-Nonlinear least squares fit of the FOMC model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 99.143 1.680 59.02 1.32e-08
-alpha 0.704 0.262 2.68 2.18e-02
-beta 64.980 36.617 1.77 6.81e-02
-
-Chi2 error estimation: 2.03 %
-
-
-
----
-Nonlinear least squares fit of the DFOP model
-
-Parameter estimation:
- Estimate Std. Error t value Pr(>t)
-parent.0 98.7514 1.33707 73.857 1.01e-07
-k1 0.0105 0.00449 2.348 3.93e-02
-k2 -0.0112 0.01884 -0.596 7.08e-01
-g 0.9390 0.18530 5.068 3.57e-03
-
-Chi2 error estimation: 1.63 %
-
-
-
----
-Endpoint estimates
-
- DT50 DT90
-SFO 106.0 352.0
-FOMC 108.9 1644.1
-DFOP 118.7 122.8
-\end{Soutput}
-\begin{Sinput}
-R> kinplot(FOCUS_2006_L4, ylab = "Observed")
-\end{Sinput}
-\end{Schunk}
-\includegraphics{examples-FOCUS_2006_L4}
-
-Although the $\chi^2$ error level is slightly smaller for the DFOP model and also
-for the FOMC model, the differences are small, and the SFO model may appear to
-be a suitable choice. The better fit of the DFOP model depends very much on the
-last three data points.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.toc b/vignettes/examples.toc
deleted file mode 100644
index af3c624..0000000
--- a/vignettes/examples.toc
+++ /dev/null
@@ -1,5 +0,0 @@
-\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}{5}{subsection.1.2}
-\contentsline {subsection}{\numberline {1.3}Laboratory Data L3}{10}{subsection.1.3}
-\contentsline {subsection}{\numberline {1.4}Laboratory Data L4}{14}{subsection.1.4}
diff --git a/vignettes/kinfit.pdf b/vignettes/kinfit.pdf
index 5fdc7c3..35bb9b8 100644
--- a/vignettes/kinfit.pdf
+++ b/vignettes/kinfit.pdf
Binary files differ

Contact - Imprint