From 73e650114af77582238abf5273e63005e0b2287e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 6 Mar 2017 17:00:48 +0100 Subject: Static documentation now built by pkgdown::build_site() --- GNUmakefile | 6 +- docs/articles/chemCal.Rnw | 130 + docs/articles/index.html | 98 + docs/authors.html | 100 + docs/calplot.lm-2.png | Bin 21681 -> 0 bytes docs/calplot.lm.html | 169 -- docs/chemCal-package.html | 99 - docs/css/bootstrap-responsive.css | 815 ----- docs/css/bootstrap-responsive.min.css | 9 - docs/css/bootstrap.css | 4983 ------------------------------- docs/css/bootstrap.min.css | 9 - docs/css/highlight.css | 28 - docs/css/staticdocs.css | 25 - docs/din32645-2.png | Bin 19858 -> 0 bytes docs/din32645.html | 188 -- docs/img/glyphicons-halflings-white.png | Bin 8777 -> 0 bytes docs/img/glyphicons-halflings.png | Bin 13826 -> 0 bytes docs/index.html | 146 +- docs/inverse.predict.html | 204 -- docs/jquery.sticky-kit.min.js | 9 + docs/js/bootstrap.js | 1825 ----------- docs/js/bootstrap.min.js | 6 - docs/link.svg | 12 + docs/lod.html | 199 -- docs/loq.html | 191 -- docs/massart97ex1.html | 102 - docs/massart97ex3-5.png | Bin 16419 -> 0 bytes docs/massart97ex3.html | 194 -- docs/pkgdown.css | 113 + docs/pkgdown.js | 8 + docs/reference.html | 118 - docs/reference/calplot-2.png | Bin 0 -> 21681 bytes docs/reference/calplot.lm.html | 177 ++ docs/reference/chemCal-package.html | 115 + docs/reference/din32645-2.png | Bin 0 -> 19858 bytes docs/reference/din32645.html | 175 ++ docs/reference/index.html | 146 + docs/reference/inverse.predict.html | 211 ++ docs/reference/lod.html | 210 ++ docs/reference/loq.html | 205 ++ docs/reference/massart97ex1.html | 118 + docs/reference/massart97ex3-5.png | Bin 0 -> 16419 bytes docs/reference/massart97ex3.html | 188 ++ docs/vignettes/chemCal.pdf | Bin 165858 -> 0 bytes 44 files changed, 2096 insertions(+), 9235 deletions(-) create mode 100644 docs/articles/chemCal.Rnw create mode 100644 docs/articles/index.html create mode 100644 docs/authors.html delete mode 100644 docs/calplot.lm-2.png delete mode 100644 docs/calplot.lm.html delete mode 100644 docs/chemCal-package.html delete mode 100644 docs/css/bootstrap-responsive.css delete mode 100644 docs/css/bootstrap-responsive.min.css delete mode 100644 docs/css/bootstrap.css delete mode 100644 docs/css/bootstrap.min.css delete mode 100644 docs/css/highlight.css delete mode 100644 docs/css/staticdocs.css delete mode 100644 docs/din32645-2.png delete mode 100644 docs/din32645.html delete mode 100644 docs/img/glyphicons-halflings-white.png delete mode 100644 docs/img/glyphicons-halflings.png delete mode 100644 docs/inverse.predict.html create mode 100644 docs/jquery.sticky-kit.min.js delete mode 100644 docs/js/bootstrap.js delete mode 100644 docs/js/bootstrap.min.js create mode 100644 docs/link.svg delete mode 100644 docs/lod.html delete mode 100644 docs/loq.html delete mode 100644 docs/massart97ex1.html delete mode 100644 docs/massart97ex3-5.png delete mode 100644 docs/massart97ex3.html create mode 100644 docs/pkgdown.css create mode 100644 docs/pkgdown.js delete mode 100644 docs/reference.html create mode 100644 docs/reference/calplot-2.png create mode 100644 docs/reference/calplot.lm.html create mode 100644 docs/reference/chemCal-package.html create mode 100644 docs/reference/din32645-2.png create mode 100644 docs/reference/din32645.html create mode 100644 docs/reference/index.html create mode 100644 docs/reference/inverse.predict.html create mode 100644 docs/reference/lod.html create mode 100644 docs/reference/loq.html create mode 100644 docs/reference/massart97ex1.html create mode 100644 docs/reference/massart97ex3-5.png create mode 100644 docs/reference/massart97ex3.html delete mode 100644 docs/vignettes/chemCal.pdf diff --git a/GNUmakefile b/GNUmakefile index d8eaa44..d01273d 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -27,10 +27,10 @@ check: build check-no-vignettes: build-no-vignettes "$(RBIN)/R" CMD check --as-cran $(TGZ) -sd: - "$(RBIN)/Rscript" -e "staticdocs::build_site()" +pd: + "$(RBIN)/Rscript" -e "pkgdown::build_site()" git add -A - git commit -m 'Static documentation rebuilt by staticdocs::build_site()' -e + git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e winbuilder: build @echo "Uploading to R-release on win-builder" diff --git a/docs/articles/chemCal.Rnw b/docs/articles/chemCal.Rnw new file mode 100644 index 0000000..30e0331 --- /dev/null +++ b/docs/articles/chemCal.Rnw @@ -0,0 +1,130 @@ +\documentclass[a4paper]{article} +%\VignetteIndexEntry{Short manual for the chemCal package} +\usepackage{hyperref} + +\title{Basic calibration functions for analytical chemistry} +\author{Johannes Ranke} + +\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/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 +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: + +<>= +library(chemCal) +data(massart97ex3) +m0 <- lm(y ~ x, data = massart97ex3) +calplot(m0) +@ + +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: + +<>= +plot(m0,which=3) +@ + +Therefore, in Example 8 in \cite{massart97} weighted regression +is proposed which can be reproduced by + +<<>>= +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) +@ + +If we now want to predict a new x value from measured y values, +we use the \texttt{inverse.predict} function: + +<<>>= +inverse.predict(m, 15, ws=1.67) +inverse.predict(m, 90, ws = 0.145) +@ + +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/docs/articles/index.html b/docs/articles/index.html new file mode 100644 index 0000000..5c6fdad --- /dev/null +++ b/docs/articles/index.html @@ -0,0 +1,98 @@ + + + + + + + + +Articles • chemCal + + + + + + + + + + + + + + + + + + + + + + + + +
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+

All vignettes

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Site built with pkgdown.

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+ + + diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 0000000..546e902 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,100 @@ + + + + + + + + +Authors • chemCal + + + + + + + + + + + + + + + + + + + + + + + + +
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    Johannes Ranke. Author, maintainer, copyright holder. +

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Site built with pkgdown.

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+ + + diff --git a/docs/calplot.lm-2.png b/docs/calplot.lm-2.png deleted file mode 100644 index 7e40a4b..0000000 Binary files a/docs/calplot.lm-2.png and /dev/null differ diff --git a/docs/calplot.lm.html b/docs/calplot.lm.html deleted file mode 100644 index 07cacd8..0000000 --- a/docs/calplot.lm.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - -calplot. chemCal 0.1-37 - - - - - - - - - - - - - - - - - - -
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Plot calibration graphs from univariate linear models

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Usage

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calplot(object, xlim = c("auto", "auto"), ylim = c("auto", "auto"),
-    xlab = "Concentration", ylab = "Response", alpha=0.05, varfunc = NULL)
- -

Arguments

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object
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- A univariate model object of class lm or - rlm - with model formula y ~ x or y ~ x - 1. -
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xlim
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- The limits of the plot on the x axis. -
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ylim
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- The limits of the plot on the y axis. -
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xlab
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- The label of the x axis. -
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ylab
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- The label of the y axis. -
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alpha
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- The error tolerance level for the confidence and prediction bands. Note that this - includes both tails of the Gaussian distribution, unlike the alpha and beta parameters - used in lod (see note below). -
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varfunc
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- The variance function for generating the weights in the model. - Currently, this argument is ignored (see note below). -
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Description

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Produce graphics of calibration data, the fitted model as well - as confidence, and, for unweighted regression, prediction bands.

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Value

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- A plot of the calibration data, of your fitted model as well as lines showing - the confidence limits. Prediction limits are only shown for models from - unweighted regression. -

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Note

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Prediction bands for models from weighted linear regression require weights - for the data, for which responses should be predicted. Prediction intervals - using weights e.g. from a variance function are currently not supported by - the internally used function predict.lm, therefore, - calplot does not draw prediction bands for such models.

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It is possible to compare the calplot prediction bands with the - lod values if the lod() alpha and beta parameters are - half the value of the calplot() alpha parameter.

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Examples

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data(massart97ex3) -m <- lm(y ~ x, data = massart97ex3) -calplot(m)
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- - \ No newline at end of file diff --git a/docs/chemCal-package.html b/docs/chemCal-package.html deleted file mode 100644 index 56a636c..0000000 --- a/docs/chemCal-package.html +++ /dev/null @@ -1,99 +0,0 @@ - - - - -chemCal-package. chemCal 0.1-37 - - - - - - - - - - - - - - - - - - -
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- Calibration functions for analytical chemistry -

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Description

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See ../DESCRIPTION

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Details

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clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} - -.sidebar h2 { - font-size: 1.1em; - padding-top: 0.5em; -} - -.sidebar li {margin-bottom: 0.5em;} diff --git a/docs/din32645-2.png b/docs/din32645-2.png deleted file mode 100644 index 1d1e8ab..0000000 Binary files a/docs/din32645-2.png and /dev/null differ diff --git a/docs/din32645.html b/docs/din32645.html deleted file mode 100644 index 8266a10..0000000 --- a/docs/din32645.html +++ /dev/null @@ -1,188 +0,0 @@ - - - - -din32645. chemCal 0.1-37 - - - - - - - - - - - - - - - - - - -
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- -

Calibration data from DIN 32645

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-
-

Usage

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data(din32645)
- -
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Description

- -

Sample dataset to test the package.

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- -
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Format

- -

A dataframe containing 10 rows of x and y values.

- -
- -
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References

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DIN 32645 (equivalent to ISO 11843), Beuth Verlag, Berlin, 1994

- -

Dintest. Plugin for MS Excel for evaluations of calibration data. Written - by Georg Schmitt, University of Heidelberg. Formerly available from - the Website of the University of Heidelberg.

- -

Currie, L. A. (1997) Nomenclature in evaluation of analytical methods including - detection and quantification capabilities (IUPAC Recommendations 1995). - Analytica Chimica Acta 391, 105 - 126.

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- -

Examples

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data(din32645) -m <- lm(y ~ x, data = din32645) -calplot(m)
-

-
-## Prediction of x with confidence interval -(prediction <- inverse.predict(m, 3500, alpha = 0.01))
-
$Prediction -[1] 0.1054792 - -$`Standard Error` -[1] 0.02215619 - -$Confidence -[1] 0.07434261 - -$`Confidence Limits` -[1] 0.03113656 0.17982178 - -
-
-# This should give 0.07434 according to test data from Dintest, which -# was collected from Procontrol 3.1 (isomehr GmbH) in this case -round(prediction$Confidence,5)
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[1] 0.07434 -
-
-## Critical value: -(crit <- lod(m, alpha = 0.01, beta = 0.5))
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$x -[1] 0.0698127 - -$y - 1 -3155.393 - -
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-# According to DIN 32645, we should get 0.07 for the critical value -# (decision limit, "Nachweisgrenze") -round(crit$x, 2)
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[1] 0.07 -
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# and according to Dintest test data, we should get 0.0698 from -round(crit$x, 4)
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[1] 0.0698 -
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-## Limit of detection (smallest detectable value given alpha and beta) -# In German, the smallest detectable value is the "Erfassungsgrenze", and we -# should get 0.14 according to DIN, which we achieve by using the method -# described in it: -lod.din <- lod(m, alpha = 0.01, beta = 0.01, method = "din") -round(lod.din$x, 2)
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[1] 0.14 -
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-## Limit of quantification -# This accords to the test data coming with the test data from Dintest again, -# except for the last digits of the value cited for Procontrol 3.1 (0.2121) -(loq <- loq(m, alpha = 0.01))
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$x -[1] 0.2119575 - -$y - 1 -4528.787 - -
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round(loq$x,4)
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[1] 0.212 -
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-# A similar value is obtained using the approximation -# LQ = 3.04 * LC (Currie 1999, p. 120) -3.04 * lod(m,alpha = 0.01, beta = 0.5)$x
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[1] 0.2122306 -
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