- 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

39 files changed, 559 insertions, 4623 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 @@
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deleted file mode 100644
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new file mode 100644
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index 84553d7..84553d7 100644
--- a/branches/0.1/chemCal/inst/doc/chemCal-002.eps
+++ b/branches/0.1/chemCal/vignettes/chemCal-002.eps
diff --git a/branches/0.1/chemCal/vignettes/chemCal-002.pdf b/branches/0.1/chemCal/vignettes/chemCal-002.pdf
new file mode 100644
index 0000000..2b56f14
--- /dev/null
+++ 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
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index e69de29..e69de29 100644
--- a/branches/0.1/chemCal/inst/doc/chemCal.bbl
+++ b/branches/0.1/chemCal/vignettes/chemCal.bbl
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index 72f5a0e..72f5a0e 100644
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index 31eced3..3107ddd 100644
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 atim and verb
 
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 \openout4 = `chemCal.out'.
 
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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
new 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
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diff --git a/trunk/chemCal/inst/doc/chemCal.pdf b/trunk/chemCal/inst/doc/chemCal.pdf
deleted file mode 100644
index c7a01d7..0000000
--- a/trunk/chemCal/inst/doc/chemCal.pdf
+++ /dev/null
diff --git a/trunk/chemCal/inst/doc/chemCal.tex b/trunk/chemCal/inst/doc/chemCal.tex
deleted file mode 100644
index 9617cda..0000000
--- a/trunk/chemCal/inst/doc/chemCal.tex
+++ /dev/null
@@ -1,169 +0,0 @@
-\documentclass[a4paper]{article}
-%\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
new 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
new 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
new 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
+++ b/trunk/chemCal/vignettes/chemCal.blg
@@ -1,4 +1,4 @@
-This is BibTeX, Version 0.99c (Web2C 7.5.4)
+This is BibTeX, Version 0.99c (TeX Live 2009/Debian)
 The top-level auxiliary file: chemCal.aux
 I found no \bibdata command---while reading file chemCal.aux
 I found no \bibstyle command---while reading file chemCal.aux
diff --git a/trunk/chemCal/vignettes/chemCal.log b/trunk/chemCal/vignettes/chemCal.log
new file mode 100644
index 0000000..2720411
--- /dev/null
+++ b/trunk/chemCal/vignettes/chemCal.log
@@ -0,0 +1,399 @@
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+entering extended mode
+ %&-line parsing enabled.
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diff --git a/trunk/chemCal/inst/doc/chemCal.out b/trunk/chemCal/vignettes/chemCal.out
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diff --git a/trunk/chemCal/vignettes/chemCal.pdf b/trunk/chemCal/vignettes/chemCal.pdf
new file mode 100644
index 0000000..5a46025
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