diff options
author | ranke <ranke@5fad18fb-23f0-0310-ab10-e59a3bee62b4> | 2012-09-11 23:56:14 +0000 |
---|---|---|
committer | ranke <ranke@5fad18fb-23f0-0310-ab10-e59a3bee62b4> | 2012-09-11 23:56:14 +0000 |
commit | b561996c588b6602b24aa1d236dee88f7c1d85a1 (patch) | |
tree | d3e4877c6b2ab0a249fba44955f2e611b69b7168 /branches | |
parent | de25b97cfa4d97f0e7c3e1e845bfa91a200b91be (diff) |
- Fixed the link to the bug report in the vignette - thanks to John Thaden for the hint
- Moved the vignette to the vignettes/ folder in order to avoid to write an .Rinstignore file
- Made the vignette compile in trunk, the trunk contains unfinished stuff however
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/chemCal@29 5fad18fb-23f0-0310-ab10-e59a3bee62b4
Diffstat (limited to 'branches')
-rw-r--r-- | branches/0.1/chemCal/DESCRIPTION | 6 | ||||
-rw-r--r-- | branches/0.1/chemCal/inst/doc/chemCal-001.pdf | 1727 | ||||
-rw-r--r-- | branches/0.1/chemCal/inst/doc/chemCal-002.pdf | 275 | ||||
-rw-r--r-- | branches/0.1/chemCal/inst/doc/chemCal.pdf | bin | 123575 -> 0 bytes | |||
-rw-r--r-- | branches/0.1/chemCal/vignettes/Makefile (renamed from branches/0.1/chemCal/inst/doc/Makefile) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/Rplots.ps (renamed from branches/0.1/chemCal/inst/doc/Rplots.ps) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-001.eps (renamed from branches/0.1/chemCal/inst/doc/chemCal-001.eps) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-001.pdf | bin | 0 -> 12038 bytes | |||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-002.eps (renamed from branches/0.1/chemCal/inst/doc/chemCal-002.eps) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-002.pdf | bin | 0 -> 5031 bytes | |||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.Rnw (renamed from branches/0.1/chemCal/inst/doc/chemCal.Rnw) | 2 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.aux (renamed from branches/0.1/chemCal/inst/doc/chemCal.aux) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.bbl (renamed from branches/0.1/chemCal/inst/doc/chemCal.bbl) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.blg (renamed from branches/0.1/chemCal/inst/doc/chemCal.blg) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.log (renamed from branches/0.1/chemCal/inst/doc/chemCal.log) | 214 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.out (renamed from branches/0.1/chemCal/inst/doc/chemCal.out) | 0 | ||||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.pdf | bin | 0 -> 179149 bytes | |||
-rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.tex (renamed from branches/0.1/chemCal/inst/doc/chemCal.tex) | 12 |
18 files changed, 154 insertions, 2082 deletions
diff --git a/branches/0.1/chemCal/DESCRIPTION b/branches/0.1/chemCal/DESCRIPTION index 323827b..ba96f47 100644 --- a/branches/0.1/chemCal/DESCRIPTION +++ b/branches/0.1/chemCal/DESCRIPTION @@ -1,6 +1,6 @@ Package: chemCal -Version: 0.1-27 -Date: 2010-09-12 +Version: 0.1-28 +Date: 2012-09-11 Title: Calibration functions for analytical chemistry Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> @@ -12,7 +12,7 @@ Description: chemCal provides simple functions for plotting linear of detection (LOQ) and limit of quantification (LOD). The functions work on model objects from - optionally weighted - linear regression (lm) or robust linear regression (rlm from the MASS package). -License: GPL version 2 or newer +License: GPL (>= 2) URL: http://www.r-project.org, http://www.uft.uni-bremen.de/chemie/ranke, http://kriemhild.uft.uni-bremen.de/viewcvs/?root=chemCal diff --git a/branches/0.1/chemCal/inst/doc/chemCal-001.pdf b/branches/0.1/chemCal/inst/doc/chemCal-001.pdf deleted file mode 100644 index fcf034d..0000000 --- a/branches/0.1/chemCal/inst/doc/chemCal-001.pdf +++ /dev/null @@ -1,1727 +0,0 @@ -%PDF-1.1 -%ρ\r -1 0 obj -<< -/CreationDate (D:20071001221414) -/ModDate (D:20071001221414) -/Title (R Graphics Output) -/Producer (R 2.6.0) -/Creator (R) ->> -endobj -2 0 obj -<< -/Type /Catalog -/Pages 3 0 R ->> -endobj -5 0 obj -<< -/Type /Font -/Subtype /Type1 -/Name /F1 -/BaseFont /ZapfDingbats ->> -endobj -6 0 obj -<< -/Type /Page -/Parent 3 0 R -/Contents 7 0 R -/Resources 4 0 R ->> -endobj -7 0 obj -<< -/Length 8 0 R ->> -stream
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+++ b/branches/0.1/chemCal/vignettes/chemCal-002.pdf diff --git a/branches/0.1/chemCal/inst/doc/chemCal.Rnw b/branches/0.1/chemCal/vignettes/chemCal.Rnw index 8cdc97c..30e0331 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.Rnw +++ b/branches/0.1/chemCal/vignettes/chemCal.Rnw @@ -22,7 +22,7 @@ At the moment, the package consists of four functions, working on univariate linear models of class \texttt{lm} or \texttt{rlm}, plus to datasets for validation. -A \href{http://bugs.r-project.org/cgi-bin/R/wishlst-fulfilled?id=8877;user=guest}{bug +A \href{http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=8877}{bug report (PR\#8877)} and the following e-mail exchange on the r-devel mailing list about prediction intervals from weighted regression entailed some further studies on this subject. However, I did not encounter any proof or explanation of the diff --git a/branches/0.1/chemCal/inst/doc/chemCal.aux b/branches/0.1/chemCal/vignettes/chemCal.aux index 20bfc98..20bfc98 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.aux +++ b/branches/0.1/chemCal/vignettes/chemCal.aux diff --git a/branches/0.1/chemCal/inst/doc/chemCal.bbl b/branches/0.1/chemCal/vignettes/chemCal.bbl index e69de29..e69de29 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.bbl +++ b/branches/0.1/chemCal/vignettes/chemCal.bbl diff --git a/branches/0.1/chemCal/inst/doc/chemCal.blg b/branches/0.1/chemCal/vignettes/chemCal.blg index 72f5a0e..72f5a0e 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.blg +++ b/branches/0.1/chemCal/vignettes/chemCal.blg diff --git a/branches/0.1/chemCal/inst/doc/chemCal.log b/branches/0.1/chemCal/vignettes/chemCal.log index 31eced3..3107ddd 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.log +++ b/branches/0.1/chemCal/vignettes/chemCal.log @@ -1,15 +1,16 @@ -This is 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(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def -File: pdftex.def 2007/01/08 v0.04d Graphics/color for pdfTeX +File: pdftex.def 2010/03/12 v0.04p Graphics/color for pdfTeX \Gread@gobject=\count94 )) \Gin@req@height=\dimen106 \Gin@req@width=\dimen107 ) (/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty -Package: fancyvrb 1998/07/17 +Package: fancyvrb 2008/02/07 -Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz) +Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix +<2008/02/07> (tvz) \FV@CodeLineNo=\count95 \FV@InFile=\read1 \FV@TabBox=\box26 \c@FancyVerbLine=\count96 \FV@StepNumber=\count97 \FV@OutFile=\write3 - -No file fancyvrb.cfg. -) (/usr/share/R/share/texmf/upquote.sty +) (/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 @@ -237,10 +297,10 @@ LaTeX Font Info: ... okay on input line 9. Package hyperref Info: Link coloring OFF on input line 9. (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty -Package: nameref 2006/12/27 v2.28 Cross-referencing by name of section +Package: nameref 2007/05/29 v2.31 Cross-referencing by name of section (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty -Package: refcount 2006/02/20 v3.0 Data extraction from references (HO) +Package: refcount 2008/08/11 v3.1 Data extraction from references (HO) ) \c@section@level=\count98 ) @@ -251,6 +311,20 @@ LaTeX Info: Redefining \pageref on input line 9. \@outlinefile=\write4 \openout4 = `chemCal.out'. +\AtBeginShipoutBox=\box27 + (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii +[Loading MPS to PDF converter (version 2006.09.02).] +\scratchcounter=\count99 +\scratchdimen=\dimen108 +\scratchbox=\box28 +\nofMPsegments=\count100 +\nofMParguments=\count101 +\everyMPshowfont=\toks16 +\MPscratchCnt=\count102 +\MPscratchDim=\dimen109 +\MPnumerator=\count103 +\everyMPtoPDFconversion=\toks17 +) LaTeX Font Info: External font `cmex10' loaded for size (Font) <12> on input line 11. LaTeX Font Info: External font `cmex10' loaded for size @@ -261,17 +335,17 @@ LaTeX Font Info: Try loading font information for T1+aett on input line 12. (/usr/share/texmf-texlive/tex/latex/ae/t1aett.fd File: t1aett.fd 1997/11/16 Font definitions for T1/aett. ) -<chemCal-001.pdf, id=9, 433.62pt x 433.62pt> +<chemCal-001.pdf, id=5, 433.62pt x 433.62pt> File: chemCal-001.pdf Graphic file (type pdf) <use chemCal-001.pdf> [1 {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] -<chemCal-002.pdf, id=21, 433.62pt x 433.62pt> +<chemCal-002.pdf, id=17, 433.62pt x 433.62pt> File: chemCal-002.pdf Graphic file (type pdf) <use chemCal-002.pdf> [2 <./chemCal-001.pdf>] LaTeX Font Info: Try loading font information for TS1+aett on input line 86. - (/usr/share/R/share/texmf/ts1aett.fd + (/usr/share/texmf/tex/latex/R/tex/latex/ts1aett.fd File: ts1aett.fd ) LaTeX Font Info: Try loading font information for TS1+cmtt on input line 86. @@ -297,29 +371,29 @@ LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) Here is how much of TeX's memory you used: - 3681 strings out of 95070 - 51909 string characters out of 1182680 - 101753 words of memory out of 1500000 - 6791 multiletter control sequences out of 10000+50000 - 21574 words of font info for 52 fonts, out of 1200000 for 2000 + 5327 strings out of 495021 + 77626 string characters out of 1181036 + 141123 words of memory out of 3000000 + 8405 multiletter control sequences out of 15000+50000 + 21574 words of font info for 52 fonts, out of 3000000 for 9000 28 hyphenation exceptions out of 8191 - 35i,7n,21p,255b,466s stack positions out of 5000i,500n,6000p,200000b,5000s -{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-super-ts1.enc}</usr/share/texmf --texlive/fonts/type1/bluesky/cm/cmbx12.pfb></usr/share/texmf-texlive/fonts/type -1/bluesky/cm/cmex10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10 -.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi5.pfb></usr/share/tex -mf-texlive/fonts/type1/bluesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/typ -e1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr12. -pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr17.pfb></usr/share/texm -f-texlive/fonts/type1/bluesky/cm/cmr5.pfb></usr/share/texmf-texlive/fonts/type1 -/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10. -pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/tex -mf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb></usr/share/texmf-texlive/fonts/ty -pe1/bluesky/cm/cmtt12.pfb></usr/share/texmf/fonts/type1/public/cm-super/sftt100 -0.pfb> -Output written on chemCal.pdf (5 pages, 123575 bytes). + 38i,7n,21p,255b,444s stack positions out of 5000i,500n,10000p,200000b,50000s + </home/ranke/.texmf-var/fonts/pk/ljfour/jknappen/ec/tctt1000.600pk></usr/sha +re/texmf-texlive/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texmf-te +xlive/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texmf-texlive/fonts +/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texmf-texlive/fonts/type1/publ +ic/amsfonts/cm/cmmi5.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/ +cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmr10.pfb +></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share +/texmf-texlive/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/share/texmf-texli +ve/fonts/type1/public/amsfonts/cm/cmr5.pfb></usr/share/texmf-texlive/fonts/type +1/public/amsfonts/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/public/amsf +onts/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/c +msy10.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmtt10.pfb>< +/usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmtt12.pfb> +Output written on chemCal.pdf (5 pages, 179149 bytes). PDF statistics: - 117 PDF objects out of 1000 (max. 8388607) - 12 named destinations out of 1000 (max. 131072) - 27 words of extra memory for PDF output out of 10000 (max. 10000000) + 115 PDF objects out of 1000 (max. 8388607) + 12 named destinations out of 1000 (max. 500000) + 11 words of extra memory for PDF output out of 10000 (max. 10000000) diff --git a/branches/0.1/chemCal/inst/doc/chemCal.out b/branches/0.1/chemCal/vignettes/chemCal.out index e69de29..e69de29 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.out +++ b/branches/0.1/chemCal/vignettes/chemCal.out diff --git a/branches/0.1/chemCal/vignettes/chemCal.pdf b/branches/0.1/chemCal/vignettes/chemCal.pdf Binary files differnew file mode 100644 index 0000000..935b160 --- /dev/null +++ b/branches/0.1/chemCal/vignettes/chemCal.pdf diff --git a/branches/0.1/chemCal/inst/doc/chemCal.tex b/branches/0.1/chemCal/vignettes/chemCal.tex index 9617cda..6326126 100644 --- a/branches/0.1/chemCal/inst/doc/chemCal.tex +++ b/branches/0.1/chemCal/vignettes/chemCal.tex @@ -5,7 +5,7 @@ \title{Basic calibration functions for analytical chemistry} \author{Johannes Ranke} -\usepackage{/usr/share/R/share/texmf/Sweave} +\usepackage{Sweave} \begin{document} \maketitle @@ -23,7 +23,7 @@ At the moment, the package consists of four functions, working on univariate linear models of class \texttt{lm} or \texttt{rlm}, plus to datasets for validation. -A \href{http://bugs.r-project.org/cgi-bin/R/wishlst-fulfilled?id=8877;user=guest}{bug +A \href{http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=8877}{bug report (PR\#8877)} and the following e-mail exchange on the r-devel mailing list about prediction intervals from weighted regression entailed some further studies on this subject. However, I did not encounter any proof or explanation of the @@ -52,7 +52,7 @@ provided by R: \begin{Schunk} \begin{Sinput} -> plot(m0, which = 3) +> plot(m0,which=3) \end{Sinput} \end{Schunk} \includegraphics{chemCal-002} @@ -66,7 +66,7 @@ is proposed which can be reproduced by > yx <- split(y, x) > ybar <- sapply(yx, mean) > s <- round(sapply(yx, sd), digits = 2) -> w <- round(1/(s^2), digits = 3) +> w <- round(1 / (s^2), digits = 3) > weights <- w[factor(x)] > m <- lm(y ~ x, w = weights) \end{Sinput} @@ -77,14 +77,14 @@ we use the \texttt{inverse.predict} function: \begin{Schunk} \begin{Sinput} -> inverse.predict(m, 15, ws = 1.67) +> inverse.predict(m, 15, ws=1.67) \end{Sinput} \begin{Soutput} $Prediction [1] 5.865367 $`Standard Error` -[1] 0.892611 +[1] 0.8926109 $Confidence [1] 2.478285 |