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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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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. 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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 diff --git a/trunk/chemCal/DESCRIPTION b/trunk/chemCal/DESCRIPTION index 6ea7b56..320ee6b 100644 --- a/trunk/chemCal/DESCRIPTION +++ b/trunk/chemCal/DESCRIPTION @@ -1,6 +1,6 @@ Package: chemCal -Version: 0.2-01 -Date: 2010-09-12 +Version: 0.2-02 +Date: 2012-09-11 Title: Calibration functions for analytical chemistry Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> diff --git a/trunk/chemCal/inst/doc/chemCal-001.pdf b/trunk/chemCal/inst/doc/chemCal-001.pdf deleted file mode 100644 index d523025..0000000 --- a/trunk/chemCal/inst/doc/chemCal-001.pdf +++ /dev/null @@ -1,1727 +0,0 @@ -%PDF-1.1 -%ρ\r -1 0 obj -<< -/CreationDate (D:20060623184130) -/ModDate (D:20060623184130) -/Title (R Graphics Output) -/Producer (R 2.3.1) -/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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-%\VignetteIndexEntry{Short manual for the chemCal package} -\usepackage{hyperref} - -\title{Basic calibration functions for analytical chemistry} -\author{Johannes Ranke} - -\usepackage{/usr/share/R/share/texmf/Sweave} -\begin{document} -\maketitle - -The \texttt{chemCal} package was first designed in the course of a lecture and lab -course on "analytics of organic trace contaminants" at the University of Bremen -from October to December 2004. In the fall 2005, an email exchange with -Ron Wehrens led to the belief that it would be desirable to implement the -inverse prediction method given in \cite{massart97} since it also covers the -case of weighted regression. Studies of the IUPAC orange book and of DIN 32645 -as well as publications by Currie and the Analytical Method Committee of the -Royal Society of Chemistry and a nice paper by Castillo and Castells provided -further understanding of the matter. - -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 -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 -formula cited below yet, so I can't really confirm that Massart's method is correct. - -When calibrating an analytical method, the first task is to generate a suitable -model. If we want to use the \texttt{chemCal} functions, we will have to restrict -ourselves to univariate, possibly weighted, linear regression so far. - -Once such a model has been created, the calibration can be graphically -shown by using the \texttt{calplot} function: - -\begin{Schunk} -\begin{Sinput} -> library(chemCal) -> data(massart97ex3) -> m0 <- lm(y ~ x, data = massart97ex3) -> calplot(m0) -\end{Sinput} -\end{Schunk} -\includegraphics{chemCal-001} - -As we can see, the scatter increases with increasing x. This is also -illustrated by one of the diagnostic plots for linear models -provided by R: - -\begin{Schunk} -\begin{Sinput} -> plot(m0, which = 3) -\end{Sinput} -\end{Schunk} -\includegraphics{chemCal-002} - -Therefore, in Example 8 in \cite{massart97} weighted regression -is proposed which can be reproduced by - -\begin{Schunk} -\begin{Sinput} -> attach(massart97ex3) -> yx <- split(y, x) -> ybar <- sapply(yx, mean) -> s <- round(sapply(yx, sd), digits = 2) -> w <- round(1/(s^2), digits = 3) -> weights <- w[factor(x)] -> m <- lm(y ~ x, w = weights) -\end{Sinput} -\end{Schunk} - -If we now want to predict a new x value from measured y values, -we use the \texttt{inverse.predict} function: - -\begin{Schunk} -\begin{Sinput} -> inverse.predict(m, 15, ws = 1.67) -\end{Sinput} -\begin{Soutput} -$Prediction -[1] 5.865367 - -$`Standard Error` -[1] 0.892611 - -$Confidence -[1] 2.478285 - -$`Confidence Limits` -[1] 3.387082 8.343652 -\end{Soutput} -\begin{Sinput} -> inverse.predict(m, 90, ws = 0.145) -\end{Sinput} -\begin{Soutput} -$Prediction -[1] 44.06025 - -$`Standard Error` -[1] 2.829162 - -$Confidence -[1] 7.855012 - -$`Confidence Limits` -[1] 36.20523 51.91526 -\end{Soutput} -\end{Schunk} - -The weight \texttt{ws} assigned to the measured y value has to be -given by the user in the case of weighted regression, or alternatively, -the approximate variance \texttt{var.s} at this location. - -\section*{Theory for \texttt{inverse.predict}} -Equation 8.28 in \cite{massart97} gives a general equation for predicting the -standard error $s_{\hat{x_s}}$ for an x value predicted from measurements of y -according to the linear calibration function $ y = b_0 + b_1 \cdot x$: - -\begin{equation} -s_{\hat{x_s}} = \frac{s_e}{b_1} \sqrt{\frac{1}{w_s m} + \frac{1}{\sum{w_i}} + - \frac{(\bar{y_s} - \bar{y_w})^2 \sum{w_i}} - {{b_1}^2 \left( \sum{w_i} \sum{w_i {x_i}^2} - - {\left( \sum{ w_i x_i } \right)}^2 \right) }} -\end{equation} - -with - -\begin{equation} -s_e = \sqrt{ \frac{\sum w_i (y_i - \hat{y_i})^2}{n - 2}} -\end{equation} - -where $w_i$ is the weight for calibration standard $i$, $y_i$ is the mean $y$ -value (!) observed for standard $i$, $\hat{y_i}$ is the estimated value for -standard $i$, $n$ is the number calibration standards, $w_s$ is the weight -attributed to the sample $s$, $m$ is the number of replicate measurements of -sample $s$, $\bar{y_s}$ is the mean response for the sample, -$\bar{y_w} = \frac{\sum{w_i y_i}}{\sum{w_i}}$ is the weighted mean of responses -$y_i$, and $x_i$ is the given $x$ value for standard $i$. - -The weight $w_s$ for the sample should be estimated or calculated in accordance -to the weights used in the linear regression. - -I adjusted the above equation in order to be able to take a different -precisions in standards and samples into account. In analogy to Equation 8.26 -from \cite{massart97} we get - -\begin{equation} -s_{\hat{x_s}} = \frac{1}{b_1} \sqrt{\frac{{s_s}^2}{w_s m} + - {s_e}^2 \left( \frac{1}{\sum{w_i}} + - \frac{(\bar{y_s} - \bar{y_w})^2 \sum{w_i}} - {{b_1}^2 \left( \sum{w_i} \sum{w_i {x_i}^2} - {\left( \sum{ w_i x_i } \right)}^2 \right) } \right) } -\end{equation} - -where I interpret $\frac{{s_s}^2}{w_s}$ as an estimator of the variance at location -$\hat{x_s}$, which can be replaced by a user-specified value using the argument -\texttt{var.s} of the function \texttt{inverse.predict}. - -\begin{thebibliography}{1} -\bibitem{massart97} -Massart, L.M, Vandenginste, B.G.M., Buydens, L.M.C., De Jong, S., Lewi, P.J., -Smeyers-Verbeke, J. -\newblock Handbook of Chemometrics and Qualimetrics: Part A, -\newblock Elsevier, Amsterdam, 1997 -\end{thebibliography} - -\end{document} diff --git a/trunk/chemCal/man/chemCal-package.Rd b/trunk/chemCal/man/chemCal-package.Rd index 4456150..fb09cb1 100644 --- a/trunk/chemCal/man/chemCal-package.Rd +++ b/trunk/chemCal/man/chemCal-package.Rd @@ -14,4 +14,3 @@ Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de> } \keyword{manip} -} diff --git a/trunk/chemCal/inst/doc/Makefile b/trunk/chemCal/vignettes/Makefile index 8eca69e..8eca69e 100644 --- a/trunk/chemCal/inst/doc/Makefile +++ b/trunk/chemCal/vignettes/Makefile diff --git a/trunk/chemCal/vignettes/Rplots.pdf b/trunk/chemCal/vignettes/Rplots.pdf Binary files differnew file mode 100644 index 0000000..4029222 --- /dev/null +++ b/trunk/chemCal/vignettes/Rplots.pdf diff --git a/trunk/chemCal/inst/doc/Rplots.ps b/trunk/chemCal/vignettes/Rplots.ps index c5e68ec..c5e68ec 100644 --- a/trunk/chemCal/inst/doc/Rplots.ps +++ b/trunk/chemCal/vignettes/Rplots.ps diff --git a/trunk/chemCal/inst/doc/chemCal-001.eps b/trunk/chemCal/vignettes/chemCal-001.eps index acc5f4b..acc5f4b 100644 --- a/trunk/chemCal/inst/doc/chemCal-001.eps +++ b/trunk/chemCal/vignettes/chemCal-001.eps diff --git a/trunk/chemCal/vignettes/chemCal-001.pdf b/trunk/chemCal/vignettes/chemCal-001.pdf Binary files differnew file mode 100644 index 0000000..a8c2629 --- /dev/null +++ b/trunk/chemCal/vignettes/chemCal-001.pdf diff --git a/trunk/chemCal/inst/doc/chemCal-002.eps b/trunk/chemCal/vignettes/chemCal-002.eps index c0ee749..c0ee749 100644 --- a/trunk/chemCal/inst/doc/chemCal-002.eps +++ b/trunk/chemCal/vignettes/chemCal-002.eps diff --git a/trunk/chemCal/vignettes/chemCal-002.pdf b/trunk/chemCal/vignettes/chemCal-002.pdf Binary files differnew file mode 100644 index 0000000..86bf0ac --- /dev/null +++ b/trunk/chemCal/vignettes/chemCal-002.pdf diff --git a/trunk/chemCal/inst/doc/chemCal.Rnw b/trunk/chemCal/vignettes/chemCal.Rnw index 956c664..3c46540 100644 --- a/trunk/chemCal/inst/doc/chemCal.Rnw +++ b/trunk/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 @@ -136,6 +136,7 @@ case. Let's take the above example and estimate a variance function <<>>= +library(doBy) massart97ex3 massart97ex3$x <- factor(massart97ex3$x) summary <- summaryBy(y~x, data = massart97ex3,FUN=c(mean,sd,var)) @@ -146,9 +147,7 @@ plot(summary$x, summary$y.var, varModel <- lm(y.var ~ I(x^2) + x, data=summary) varCurve <- predict(varModel, newdata=data.frame(x=0:5000/100)) lines(0:5000/100,varCurve) - - - +@ \begin{thebibliography}{1} diff --git a/trunk/chemCal/inst/doc/chemCal.aux b/trunk/chemCal/vignettes/chemCal.aux index 20bfc98..20bfc98 100644 --- a/trunk/chemCal/inst/doc/chemCal.aux +++ b/trunk/chemCal/vignettes/chemCal.aux diff --git a/trunk/chemCal/inst/doc/chemCal.bbl b/trunk/chemCal/vignettes/chemCal.bbl index e69de29..e69de29 100644 --- a/trunk/chemCal/inst/doc/chemCal.bbl +++ b/trunk/chemCal/vignettes/chemCal.bbl diff --git a/trunk/chemCal/inst/doc/chemCal.blg b/trunk/chemCal/vignettes/chemCal.blg index 72f5a0e..2904a63 100644 --- a/trunk/chemCal/inst/doc/chemCal.blg +++ 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