First import, for archiving purposes.

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/chemCal@1 5fad18fb-23f0-0310-ab10-e59a3bee62b4

22 files changed, 834 insertions, 0 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
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index 0000000..18bcf09
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,12 @@
+Package: chemCal
+Version: 0.03-1
+Date: 2005-01-14
+Title: Calibration for analytical chemistry
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Maintainer: Johannes Ranke <jranke@uni-bremen.de>
+Depends: R
+Description: chemCal provides simple functions for plotting
+	calibration functions and for estimating standard errors for measurements.
+License: GPL version 2 or newer
+URL: http://www.r-project.org, 
+	http://www.uft.uni-bremen.de/chemie/ranke
diff --git a/INDEX b/INDEX
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index 0000000..ec2f1b4
--- /dev/null
+++ b/INDEX
@@ -0,0 +1,10 @@
+calm					Generate a linear calibration model
+calplot                 Plot calibration graphs
+plot.calm				Plot prediction bands
+calpredict              Estimate measurement results including
+                        confidence intervals
+predict.calm			Estimate measurement results including confidence 
+						intervals
+din32645                Calibration data from DIN 32645
+pahCalibration          Calibration data for HPLC measurement of 4 PAH
+pahMeasurements			Measurement data for HPLC measurement of 4 PAH
diff --git a/R/chemCal.R b/R/chemCal.R
new file mode 100644
index 0000000..5de33f8
--- /dev/null
+++ b/R/chemCal.R
@@ -0,0 +1,195 @@
+calm <- function(data)
+{
+    y <- data[[2]]
+    x <- data[[1]]
+    m <- lm(y ~ x)
+    s <- summary(m)
+    if (s$coefficients[1,4] > 0.05) 
+    {
+        m <- lm(y ~ x - 1)
+        s <- summary(m)
+        m$intercept <- FALSE
+    } else {
+        m$intercept <- TRUE
+    }
+    class(m) <- "calm"
+    m$yname <- names(data)[[1]]
+    m$xname <- names(data)[[2]]
+    return(m)    
+}
+predict.calm <- predict.lm
+print.calm <- print.lm
+summary.calm <- summary.lm
+plot.calm <- function(m,
+    xunit="",yunit="",measurand="",
+    level=0.95)
+{
+    x <- m$model$x
+    y <- m$model$y
+    newdata <- data.frame(x = seq(0,max(x),length=250))
+    pred.lim <- predict(m, newdata, interval = "prediction",level=level)
+    conf.lim <- predict(m, newdata, interval = "confidence",level=level)
+    if (xunit!="") {
+        xlab <- paste("Concentration in ",xunit)
+    } else xlab <- m$xname
+    if (yunit=="") yunit <- m$yname
+    if (measurand!="") {
+        main <- paste("Calibration for",measurand)
+    } else main <- "Calibration"
+    plot(1,
+        xlab = xlab,
+        ylab = yunit,
+        type = "n", 
+        main = main,
+        xlim = c(0,max(x)), 
+        ylim = range(pred.lim)
+    )
+    points(x,y, pch = 21, bg = "yellow")
+    matlines(newdata$x, pred.lim, lty = c(1, 4, 4), 
+        col = c("black", "red", "red"))
+    matlines(newdata$x, conf.lim, lty = c(1, 3, 3), 
+        col = c("black", "green4", "green4"))
+
+    legend(min(x), 
+        max(pred.lim, na.rm = TRUE), 
+        legend = c("Fitted Line", "Confidence Bands", 
+            "Prediction Bands"), 
+        lty = c(1, 3, 4), 
+        lwd = 2, 
+        col = c("black", "green4", "red"), 
+        horiz = FALSE, cex = 0.9, bg = "gray95")
+}
+predictx.calm <- function(m,measurements)
+{
+    s <- summary(m)    
+    xi <- m$model$x
+    yi <- m$model$y
+    n <- length(yi)
+    yobs <- newdata[[1]]
+    p <- length(yobs)
+    if (!m$intercept)
+    {
+        varb1 <- summary(m)$coef["x","Std. Error"]^2
+        xpred <- mean(yobs)/b1
+        varxpred <- (varyobs + xpred^2 * varb1) / b1^2
+        sdxpred <- sqrt(varxpred) 
+    } else 
+    {
+        b0 <- summary(m)$coef["(Intercept)","Estimate"]
+        b1 <- summary(m)$coef["xi","Estimate"]
+        xpred <- (mean(yobs) - b0)/b1
+        sumxxbar <- sum((xi - mean(xi))^2) 
+        if (!syobs)
+        {
+            yybar <- (mean(yobs) - mean(yi))^2
+            sdxpred <- (S/b1) * (1/p + 1/n + yybar/(b1^2 * sumxxbar))^0.5
+        } else
+        {
+            sdxpred <- ((varyobs^0.5/b1) + (S/b1)^2 * (1/n + ((xpred - mean(xi))^2)/sumxxbar))^0.5
+        }
+    }
+    t <- qt((1 + level)/2,ntot - 2)
+    confxpred <- t * sdxpred
+
+    result <- c(estimate=xpred,sdxpred=sdxpred,syobs=syobs,
+        confxpred=confxpred)
+    digits <- max(c(3,round(log10(xpred/confxpred)) + 2))
+    roundedresult <- round(result,digits=digits)
+    confidenceinterval <- paste(roundedresult["estimate"],"+-",
+        roundedresult["confxpred"],xunit)
+    roundedresult[["confidenceinterval"]] <- confidenceinterval
+    invisible(roundedresult)
+}
+calpredict <- function(yobs,xi,yi,xunit="",level=0.95,intercept=FALSE,syobs=FALSE)
+{
+    if (length(xi)!=length(yi))
+    {
+        cat("xi and yi have to be of the same length\n")
+    }
+    xi <- xi[!is.na(yi)]
+    yi <- yi[!is.na(yi)]
+    n <- length(yi)
+    p <- length(yobs)
+    if (!intercept)
+    {
+        m <- lm(yi ~ xi - 1)
+    } else 
+    {
+        m <- lm(yi ~ xi)
+    }
+    S <- summary(m)$sigma
+    b1 <- summary(m)$coef["xi","Estimate"]
+
+    if (syobs)
+    {
+        if (is.numeric(syobs))
+        {
+            varyobs <- syobs^2
+            ntot <- n
+        } else
+        {
+            if (length(yobs)==1)
+            {
+                cat("yobs has to contain more than one number vector, if you use syobs=TRUE\n")
+            }
+            varyobs <- var(yobs)
+            ntot <- n + p
+        }
+    } else
+    {
+        varyobs <- S^2
+        ntot <- n
+    }
+
+    if (!intercept)
+    {
+        varb1 <- summary(m)$coef["xi","Std. Error"]^2
+        xpred <- mean(yobs)/b1
+        varxpred <- (varyobs + xpred^2 * varb1) / b1^2
+        sdxpred <- sqrt(varxpred) 
+    } else 
+    {
+        b0 <- summary(m)$coef["(Intercept)","Estimate"]
+        b1 <- summary(m)$coef["xi","Estimate"]
+        xpred <- (mean(yobs) - b0)/b1
+        sumxxbar <- sum((xi - mean(xi))^2) 
+        if (!syobs)
+        {
+            yybar <- (mean(yobs) - mean(yi))^2
+            sdxpred <- (S/b1) * (1/p + 1/n + yybar/(b1^2 * sumxxbar))^0.5
+        } else
+        {
+            sdxpred <- ((varyobs^0.5/b1) + (S/b1)^2 * (1/n + ((xpred - mean(xi))^2)/sumxxbar))^0.5
+        }
+    }
+    t <- qt((1 + level)/2,ntot - 2)
+    confxpred <- t * sdxpred
+
+    result <- c(estimate=xpred,sdxpred=sdxpred,syobs=syobs,
+        confxpred=confxpred)
+    digits <- max(c(3,round(log10(xpred/confxpred)) + 2))
+    roundedresult <- round(result,digits=digits)
+    confidenceinterval <- paste(roundedresult["estimate"],"+-",
+        roundedresult["confxpred"],xunit)
+    roundedresult[["confidenceinterval"]] <- confidenceinterval
+    invisible(roundedresult)
+}
+
+multical <- function(cf,df,intercept=FALSE)
+{
+    rf <- data.frame(name=levels(df$name))
+    substances <- colnames(df)[-1]
+    for (s in substances)
+    {
+        r <- vector()
+        for (sample in levels(df$name))
+        {
+            tmp <- calpredict(subset(df,name==sample)[[s]],
+                cf[["conc"]],cf[[s]],
+                intercept=intercept)
+            r <- c(r,tmp[["confidenceinterval"]])
+        }
+        rf[[s]] <- r
+    }
+    return(rf)
+}
diff --git a/chm/00Index.html b/chm/00Index.html
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--- /dev/null
+++ b/chm/00Index.html
@@ -0,0 +1,26 @@
+<html><head><title>Calibration for analytical chemistry</title>

+<link rel="stylesheet" type="text/css" href="Rchm.css">

+</head><body>

+<h1>Calibration for analytical chemistry

+<img class="toplogo" src="logo.jpg" alt="[R logo]"></h1>

+

+<hr>

+

+<object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

+<param name="keyword" value=".. contents">

+</object>

+

+<h2>Help pages for package `chemCal' version 0.01-2</h2>

+

+

+<table width="100%">

+<tr><td width="25%"><a href="calplot.html">calplot</a></td>

+<td>Plot calibration graphs</td></tr>

+<tr><td width="25%"><a href="calpredict.html">calpredict</a></td>

+<td>Estimate measurement results including confidence intervals</td></tr>

+<tr><td width="25%"><a href="din32645.html">din32645</a></td>

+<td>Calibration data from DIN 32645</td></tr>

+<tr><td width="25%"><a href="pahCalibration.html">pahCalibration</a></td>

+<td>Calibration data for HPLC measurement of 4 PAH</td></tr>

+</table>

+</body></html>

diff --git a/chm/Rchm.css b/chm/Rchm.css
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index 0000000..badd579
--- /dev/null
+++ b/chm/Rchm.css
@@ -0,0 +1,25 @@
+BODY{		background: white;
+		color: black }
+
+A:link{         background: white;
+                color: blue }
+A:visited{	background: white;
+		color: rgb(50%, 0%, 50%) }
+
+H1{		background: white;
+		color: rgb(55%, 55%, 55%);
+		font-family: monospace;
+		font-size: large;
+		text-align: center }
+
+H2{		background: white;
+		color: rgb(0%, 0%, 100%);
+		font-family: monospace;
+		text-align: center }
+
+H3{		background: white;
+		color: rgb(40%, 40%, 40%);
+		font-family: monospace }
+
+IMG.toplogo{	vertical-align: middle }
+
diff --git a/chm/calplot.html b/chm/calplot.html
new file mode 100755
index 0000000..a2b8158
--- /dev/null
+++ b/chm/calplot.html
@@ -0,0 +1,94 @@
+<html><head><title>Plot calibration graphs</title>

+<link rel="stylesheet" type="text/css" href="Rchm.css">

+</head>

+<body>

+

+<table width="100%"><tr><td>calplot(chemCal)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

+<param name="keyword" value="R:   calplot">

+<param name="keyword" value=" Plot calibration graphs">

+</object>

+

+

+<h2>Plot calibration graphs</h2>

+

+

+<h3>Description</h3>

+

+<p>

+Produce graphics of calibration data, the fitted model as well

+as prediction and confidence intervals.

+</p>

+

+

+<h3>Usage</h3>

+

+<pre>

+  calplot(x,y,intercept=FALSE,measurand="substance x",xunit="mg/L",yunit="Area",level=0.95)

+</pre>

+

+

+<h3>Arguments</h3>

+

+<table summary="R argblock">

+<tr valign="top"><td><code>x</code></td>

+<td>

+A vector of x values.

+</td></tr>

+<tr valign="top"><td><code>y</code></td>

+<td>

+A vector of y values.

+</td></tr>

+<tr valign="top"><td><code>intercept</code></td>

+<td>

+A boolean describing if the calibration curve is to be forced

+through zero.

+</td></tr>

+<tr valign="top"><td><code>measurand</code></td>

+<td>

+The name of what is being measured as a character vector.

+</td></tr>

+<tr valign="top"><td><code>xunit</code></td>

+<td>

+The unit of the given values on the x axis as a character vector.

+</td></tr>

+<tr valign="top"><td><code>yunit</code></td>

+<td>

+The unit of the y axis as a character vector. Defaults to "Area".

+</td></tr>

+<tr valign="top"><td><code>level</code></td>

+<td>

+The confidence level of the confidence and prediction bands. Defaults to

+0.95.

+</td></tr>

+</table>

+

+<h3>Value</h3>

+

+<p>

+A linear model object for y ~ x.  You will also get a plot of the calibration

+data, of your fitted model as well as lines showing the confidence limits and

+the prediction limits.</p>

+

+<h3>Author(s)</h3>

+

+<p>

+Johannes Ranke 

+<a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a> 

+<a href="http://www.uft.uni-bremen.de/chemie/ranke">http://www.uft.uni-bremen.de/chemie/ranke</a>

+</p>

+

+

+<h3>Examples</h3>

+

+<pre>

+data(pahCalibration)

+attach(pahCalibration)

+## Not run: calplot(conc,phenanthrene,"Phenanthrene","mg/L")

+detach(pahCalibration)

+</pre>

+

+

+

+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

+

+</body></html>

diff --git a/chm/calpredict.html b/chm/calpredict.html
new file mode 100755
index 0000000..dff8ec4
--- /dev/null
+++ b/chm/calpredict.html
@@ -0,0 +1,106 @@
+<html><head><title>Estimate measurement results including confidence intervals</title>

+<link rel="stylesheet" type="text/css" href="Rchm.css">

+</head>

+<body>

+

+<table width="100%"><tr><td>calpredict(chemCal)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

+<param name="keyword" value="R:   calpredict">

+<param name="keyword" value=" Estimate measurement results including confidence intervals">

+</object>

+

+

+<h2>Estimate measurement results including confidence intervals</h2>

+

+

+<h3>Description</h3>

+

+<p>

+This function generates estimates for x values from y values, including

+a confidence interval for the x values.  The formulas in this function used

+for prediction of concentrations from (replicate) measurements are taken from 

+the "Handbook of Chemometrics and Qualimetrics Part A" by D. L. Massart, 

+Vandeginste, B. G. M., Buydens, L. M. C., De Jong, S., Lewi, P. J. and

+Smeyers-Verbeke, J, Elsevier, Amsterdam, 1997 and from the EURACHEM/CITAC

+report on "Quantifying uncertainty in analytical measurement", 2000, 

+pp. 111f.

+</p>

+

+

+<h3>Usage</h3>

+

+<pre>

+  calpredict(yobs,xi,yi,xunit="",level=0.95,intercept=FALSE,syobs=FALSE)

+</pre>

+

+

+<h3>Arguments</h3>

+

+<table summary="R argblock">

+<tr valign="top"><td><code>yobs</code></td>

+<td>

+A numeric vector containing the observed data.

+</td></tr>

+<tr valign="top"><td><code>xi</code></td>

+<td>

+A vector of x values of the calibration. 

+</td></tr>

+<tr valign="top"><td><code>yi</code></td>

+<td>

+A vector of y values of the calibration. 

+</td></tr>

+<tr valign="top"><td><code>xunit</code></td>

+<td>

+The unit of the given values on the x axis as a character string.

+</td></tr>

+<tr valign="top"><td><code>level</code></td>

+<td>

+The desired confidence level for the confidence interval of the

+estimates. Defaults to 0.95.

+</td></tr>

+<tr valign="top"><td><code>intercept</code></td>

+<td>

+Logical value determining if an intercept is to be fitted or not. 

+Default is FALSE.

+</td></tr>

+<tr valign="top"><td><code>syobs</code></td>

+<td>

+If TRUE, a standard deviation for the given y values is 

+calculated, and the resulting confidence interval will

+include this variability (not validated yet). If FALSE (default), this

+standard deviation is not included in the 

+confidence interval. If a numeric value is given, 

+it is used for the standard deviation of "real samples",

+in addition to the standard deviation of the y values

+in the calibration (also not validated yet).

+</td></tr>

+</table>

+

+<h3>Value</h3>

+

+<p>

+A list containing the estimate, its standard deviation and its 

+confidence interval.</p>

+

+<h3>Author(s)</h3>

+

+<p>

+Johannes Ranke 

+<a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a> 

+<a href="http://www.uft.uni-bremen.de/chemie/ranke">http://www.uft.uni-bremen.de/chemie/ranke</a>

+</p>

+

+

+<h3>Examples</h3>

+

+<pre>

+data(pahCalibration)

+attach(pahCalibration)

+y &lt;- c(51.2,51.4,51.1,51.8)

+estimate &lt;- calpredict(y,conc,acenaphthene,xunit="mg/L")

+</pre>

+

+

+

+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

+

+</body></html>

diff --git a/chm/chemCal.chm b/chm/chemCal.chm
new file mode 100755
index 0000000..df88b92
--- /dev/null
+++ b/chm/chemCal.chm
diff --git a/chm/chemCal.hhp b/chm/chemCal.hhp
new file mode 100755
index 0000000..3b1318b
--- /dev/null
+++ b/chm/chemCal.hhp
@@ -0,0 +1,17 @@
+[OPTIONS]

+Auto Index=Yes

+Contents file=chemCal.toc

+Compatibility=1.1 or later

+Compiled file=chemCal.chm

+Default topic=00Index.html

+Display compile progress=No

+Full-text search=Yes

+Full text search stop list file=..\..\..\gnuwin32\help\R.stp

+

+

+[FILES]

+00Index.html

+calplot.html

+calpredict.html

+din32645.html

+pahCalibration.html

diff --git a/chm/chemCal.toc b/chm/chemCal.toc
new file mode 100755
index 0000000..ab7c2f1
--- /dev/null
+++ b/chm/chemCal.toc
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">

+<HEAD></HEAD><HTML><BODY>

+<UL>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Package chemCal:  Contents">

+<param name="Local" value="00Index.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Package chemCal:  R objects">

+</OBJECT>

+<UL>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="calplot">

+<param name="Local" value="calplot.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="calpredict">

+<param name="Local" value="calpredict.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="din32645">

+<param name="Local" value="din32645.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="pahCalibration">

+<param name="Local" value="pahCalibration.html">

+</OBJECT>

+</UL>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Package chemCal:  Titles">

+</OBJECT>

+<UL>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Calibration data for HPLC measurement of 4 PAH">

+<param name="Local" value="pahCalibration.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Calibration data from DIN 32645">

+<param name="Local" value="din32645.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Estimate measurement results including confidence intervals">

+<param name="Local" value="calpredict.html">

+</OBJECT>

+<LI> <OBJECT type="text/sitemap">

+<param name="Name" value="Plot calibration graphs">

+<param name="Local" value="calplot.html">

+</OBJECT>

+</UL>

+</UL>

+</BODY></HTML>

diff --git a/chm/din32645.html b/chm/din32645.html
new file mode 100755
index 0000000..f0550f7
--- /dev/null
+++ b/chm/din32645.html
@@ -0,0 +1,44 @@
+<html><head><title>Calibration data from DIN 32645</title>

+<link rel="stylesheet" type="text/css" href="Rchm.css">

+</head>

+<body>

+

+<table width="100%"><tr><td>din32645(chemCal)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

+<param name="keyword" value="R:   din32645">

+<param name="keyword" value=" Calibration data from DIN 32645">

+</object>

+

+

+<h2>Calibration data from DIN 32645</h2>

+

+

+<h3>Description</h3>

+

+<p>

+Sample dataset to test the package.

+</p>

+

+

+<h3>Usage</h3>

+

+<pre>data(pahCalibration)</pre>

+

+

+<h3>Format</h3>

+

+<p>

+A dataframe containing 10 rows of x and y values.

+</p>

+

+

+<h3>Source</h3>

+

+<p>

+<a href="http://www.uft.uni-bremen.de/chemie">http://www.uft.uni-bremen.de/chemie</a>

+</p>

+

+

+

+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

+

+</body></html>

diff --git a/chm/logo.jpg b/chm/logo.jpg
new file mode 100755
index 0000000..b8e2149
--- /dev/null
+++ b/chm/logo.jpg
diff --git a/chm/pahCalibration.html b/chm/pahCalibration.html
new file mode 100755
index 0000000..10d1774
--- /dev/null
+++ b/chm/pahCalibration.html
@@ -0,0 +1,48 @@
+<html><head><title>Calibration data for HPLC measurement of 4 PAH</title>

+<link rel="stylesheet" type="text/css" href="Rchm.css">

+</head>

+<body>

+

+<table width="100%"><tr><td>pahCalibration(chemCal)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

+<param name="keyword" value="R:   pahCalibration">

+<param name="keyword" value=" Calibration data for HPLC measurement of 4 PAH">

+</object>

+

+

+<h2>Calibration data for HPLC measurement of 4 PAH</h2>

+

+

+<h3>Description</h3>

+

+<p>

+This dataset was produced during a course on trace analysis

+of organic contaminants. The data are far from perfect, but 

+good enough to serve as an example.

+</p>

+

+

+<h3>Usage</h3>

+

+<pre>data(pahCalibration)</pre>

+

+

+<h3>Format</h3>

+

+<p>

+A dataframe containing the areas for the four polycyclic aromatic

+hydrocarbons (PAH) Acenaphthene, Phenanthrene, Anthracene and Pyrene.

+Each measurement of a standard solution makes up one row.

+</p>

+

+

+<h3>Source</h3>

+

+<p>

+<a href="http://www.uft.uni-bremen.de/chemie">http://www.uft.uni-bremen.de/chemie</a>

+</p>

+

+

+

+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

+

+</body></html>

diff --git a/data/din32645.rda b/data/din32645.rda
new file mode 100644
index 0000000..4e2913a
--- /dev/null
+++ b/data/din32645.rda
diff --git a/data/pahCalibration.rda b/data/pahCalibration.rda
new file mode 100644
index 0000000..a0ae738
--- /dev/null
+++ b/data/pahCalibration.rda
diff --git a/data/pahMeasurements.rda b/data/pahMeasurements.rda
new file mode 100644
index 0000000..657e552
--- /dev/null
+++ b/data/pahMeasurements.rda
diff --git a/man/calplot.Rd b/man/calplot.Rd
new file mode 100644
index 0000000..7500912
--- /dev/null
+++ b/man/calplot.Rd
@@ -0,0 +1,52 @@
+\name{calplot}
+\alias{calplot}
+\title{Plot calibration graphs}
+\description{
+	Produce graphics of calibration data, the fitted model as well
+  as prediction and confidence intervals.
+}
+\usage{
+  calplot(x,y,intercept=FALSE,measurand="substance x",xunit="mg/L",yunit="Area",level=0.95)
+}
+\arguments{
+  \item{x}{
+    A vector of x values.
+    }
+  \item{y}{
+    A vector of y values.
+    }
+  \item{intercept}{
+    A boolean describing if the calibration curve is to be forced
+    through zero.
+    }
+  \item{measurand}{ 
+    The name of what is being measured as a character vector.
+    }
+  \item{xunit}{
+    The unit of the given values on the x axis as a character vector.
+    }
+  \item{yunit}{
+    The unit of the y axis as a character vector. Defaults to "Area".
+    }
+  \item{level}{
+    The confidence level of the confidence and prediction bands. Defaults to
+    0.95.
+    }
+}
+\value{
+  A linear model object for y ~ x.  You will also get a plot of the calibration
+  data, of your fitted model as well as lines showing the confidence limits and
+  the prediction limits.
+} 
+\examples{
+data(pahCalibration)
+attach(pahCalibration)
+\dontrun{calplot(conc,phenanthrene,"Phenanthrene","mg/L")}
+detach(pahCalibration)
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{regression}
diff --git a/man/calpredict.Rd b/man/calpredict.Rd
new file mode 100644
index 0000000..a91d018
--- /dev/null
+++ b/man/calpredict.Rd
@@ -0,0 +1,64 @@
+\name{calpredict}
+\alias{calpredict}
+\title{Estimate measurement results including confidence intervals}
+\description{
+  This function generates estimates for x values from y values, including
+  a confidence interval for the x values.  The formulas in this function used
+  for prediction of concentrations from (replicate) measurements are taken from 
+  the "Handbook of Chemometrics and Qualimetrics Part A" by D. L. Massart, 
+  Vandeginste, B. G. M., Buydens, L. M. C., De Jong, S., Lewi, P. J. and
+  Smeyers-Verbeke, J, Elsevier, Amsterdam, 1997 and from the EURACHEM/CITAC
+  report on "Quantifying uncertainty in analytical measurement", 2000, 
+  pp. 111f.
+}
+\usage{
+  calpredict(yobs,xi,yi,xunit="",level=0.95,intercept=FALSE,syobs=FALSE)
+}
+\arguments{
+  \item{yobs}{ 
+    A numeric vector containing the observed data.
+    }
+  \item{xi}{
+    A vector of x values of the calibration. 
+    }
+  \item{yi}{
+    A vector of y values of the calibration. 
+    }
+  \item{xunit}{ 
+    The unit of the given values on the x axis as a character string.
+    }
+  \item{level}{ 
+    The desired confidence level for the confidence interval of the
+    estimates. Defaults to 0.95.
+    }
+  \item{intercept}{ 
+    Logical value determining if an intercept is to be fitted or not. 
+    Default is FALSE.
+    }
+  \item{syobs}{ 
+    If TRUE, a standard deviation for the given y values is 
+    calculated, and the resulting confidence interval will
+    include this variability (not validated yet). If FALSE (default), this
+    standard deviation is not included in the 
+    confidence interval. If a numeric value is given, 
+    it is used for the standard deviation of "real samples",
+    in addition to the standard deviation of the y values
+    in the calibration (also not validated yet).
+    }
+}
+\value{
+  A list containing the estimate, its standard deviation and its 
+  confidence interval.
+} 
+\examples{
+data(pahCalibration)
+attach(pahCalibration)
+y <- c(51.2,51.4,51.1,51.8)
+estimate <- calpredict(y,conc,acenaphthene,xunit="mg/L")
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{regression}
diff --git a/man/din32645.Rd b/man/din32645.Rd
new file mode 100644
index 0000000..901bdf0
--- /dev/null
+++ b/man/din32645.Rd
@@ -0,0 +1,15 @@
+\name{din32645}
+\docType{data}
+\alias{din32645}
+\title{Calibration data from DIN 32645}
+\description{
+  Sample dataset to test the package.
+}
+\usage{data(pahCalibration)}
+\format{
+  A dataframe containing 10 rows of x and y values.
+}
+\source{
+  \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/multical.Rd b/man/multical.Rd
new file mode 100644
index 0000000..7d62277
--- /dev/null
+++ b/man/multical.Rd
@@ -0,0 +1,37 @@
+\name{multical}
+\alias{multical}
+\title{Calculation of results in a dataframe}
+\description{
+  This function provides the possibility to perform the calibration
+  of multiple components simultaneously, and to provide the results
+  including confidence intervals in a dataframe.
+}
+\usage{
+  multical(cf,df,intercept=FALSE)
+}
+\arguments{
+  \item{cf}{ 
+    A data frame containig the data for the calibration standards.
+    }
+  \item{df}{
+    A data frame with the measured sample data.
+    }
+  \item{intercept}{ 
+    Logical value determining if an intercept is to be fitted or not. 
+    Default is FALSE.
+    }
+}
+\value{
+  A data frame containig the measurement results with a confidence interval.
+} 
+\examples{
+data(pahCalibration)
+data(pahMeasurements)
+result <- multical(pahCalibration,pahMeasurements)
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{regression}
diff --git a/man/pahCalibration.Rd b/man/pahCalibration.Rd
new file mode 100644
index 0000000..540af4a
--- /dev/null
+++ b/man/pahCalibration.Rd
@@ -0,0 +1,19 @@
+\name{pahCalibration}
+\docType{data}
+\alias{pahCalibration}
+\title{Calibration data for HPLC measurement of 4 PAH}
+\description{
+  This dataset was produced during a course on trace analysis
+  of organic contaminants. The data are far from perfect, but 
+  good enough to serve as an example.
+}
+\usage{data(pahCalibration)}
+\format{
+  A dataframe containing the areas for the four polycyclic aromatic
+  hydrocarbons (PAH) Acenaphthene, Phenanthrene, Anthracene and Pyrene.
+  Each measurement of a standard solution makes up one row.
+}
+\source{
+  \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/pahMeasurements.Rd b/man/pahMeasurements.Rd
new file mode 100644
index 0000000..77b646b
--- /dev/null
+++ b/man/pahMeasurements.Rd
@@ -0,0 +1,19 @@
+\name{pahMeasurements}
+\docType{data}
+\alias{pahMeasurements}
+\title{Measurement data for HPLC measurement of 4 PAH}
+\description{
+  This dataset was produced during a course on trace analysis
+  of organic contaminants. The data are far from perfect, but 
+  good enough to serve as an example.
+}
+\usage{data(pahMeasurements)}
+\format{
+  A dataframe containing the areas for the four polycyclic aromatic
+  hydrocarbons (PAH) Acenaphthene, Phenanthrene, Anthracene and Pyrene
+  in the different samples.
+}
+\source{
+  \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}