version 0.1-5

DESCRIPTION

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+Package: kulife
+Version: 0.1-5
+Title: Data sets and functions from the Faculty of Life Sciences,
+        University of Copenhagen
+Author: Claus Ekstrom <ekstrom@life.ku.dk>, Ib M. Skovgaard
+        <ims@life.ku.dk>, Torben Martinussen <tma@life.ku.dk>
+Maintainer: Claus Ekstrom <ekstrom@life.ku.dk>
+Enhances: XML
+Description: Provides various functions and data sets from experiments
+        at the Faculty of Life Sciences, University of Copenhagen
+License: GPL-2
+Packaged: 2011-04-11 19:17:53 UTC; claus
+Repository: CRAN
+Date/Publication: 2011-04-12 06:22:23

R/rootonorm.r

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+rootonorm <- function(x, breaks="Sturges",
+                      type=c("hanging", "deviation"),
+                      scale=c("sqrt", "raw"),
+                      zeroline=TRUE,                      
+                      linecol="red", rectcol="lightgrey",
+                      xlab=xname,
+                      ylab="Sqrt(frequency)",
+                      ylim=NULL,
+                      mu=mean(x), s=sd(x),
+                      gap=0.1, ...) {
+
+
+  if (!is.numeric(x)) 
+    stop("'x' must be numeric")
+
+  # Fix the xlabel if it isn't specified
+  xname <- deparse(substitute(x))
+
+  scale <- match.arg(scale)
+  if (is.character(scale) && scale == "raw") {
+    scale <- match.fun("as.numeric")
+    if (missing(ylab)) {
+      ylab <- "Frequency"
+    }
+  }
+  else {
+    scale <- match.fun(scale)
+  } 
+
+  type <- match.arg(type)
+
+  h <- hist(x, breaks=breaks, plot=FALSE)
+  if (!h$equidist) stop("breaks must be equally spaced")
+
+  nbins <- length(h$counts)
+  nobs <- sum(h$counts)
+
+  expected <- nobs*diff(pnorm(h$breaks, mu, s))
+
+  d.gap <- min(diff(h$breaks)) * gap /2
+
+  plot.range <- range(pretty(h$breaks))  
+  z <- seq(plot.range[1], plot.range[2], length.out=200)
+  z.y <- min(diff(h$breaks))*nobs*dnorm(z, mu, s)
+
+  minval <- min(scale(expected)-scale(h$counts))
+
+  if (is.null(ylim)) {
+    ylim <- c(minval, scale(max(expected,z.y)))
+  }
+
+  plot(z, z, type="n",
+       xlab=xlab,
+       ylab=ylab,
+       yaxt="n",
+       ylim=ylim,
+       ...)
+
+  if (type=="deviation") {  
+    for(i in 1:nbins) {
+      rect(h$breaks[i]+d.gap, scale(expected[i])-scale(h$counts[i]),
+           h$breaks[i+1]-d.gap, 0, col=rectcol)
+    }    
+  }
+  else {
+    for(i in 1:nbins) {
+      rect(h$breaks[i]+d.gap, scale(expected[i])-scale(h$counts[i]),
+           h$breaks[i+1]-d.gap, scale(expected[i]), col=rectcol)
+    }
+  }
+
+  lines(z, scale(z.y), col=linecol, ...)
+  if (zeroline) {
+    abline(h=0, lty=3)
+  }
+  return(h$counts)
+}

R/writexml.R

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+write.xml <- function(data, file=NULL) {
+#  require(XML)
+
+  # Check that packages is available
+  if (! "XML" %in% row.names(installed.packages()) )
+    stop("package XML must be installed")
+
+  if(is.null(file))
+    stop("filename not specified")
+
+  if (!is.data.frame(data))
+    stop("data must be a data frame")
+
+  # Start empty XML document tree
+  doc <- XML:::newXMLDoc()          
+  # Start by adding a document tag at the root of the XML file
+  root <- XML:::newXMLNode("document", doc=doc)
+
+  # Make output invisible
+  invisible(
+    # Iterate over all rows
+    lapply(1:nrow(data),                 
+           function(rowi) {
+             r <- XML:::newXMLNode("row", parent=root)   # Create row tag
+             for(var in names(data)) {   # Iterate over variables
+               XML:::newXMLNode(var, data[rowi, var], parent = r)
+             }
+           }))            
+  invisible(XML:::saveXML(doc, file=file))
+}

build/qpcr.r

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+# Hent read.xls
+
+library(gdata)
+
+indata <- read.xls("qpcr.xls", header=TRUE)
+
+
+cycle <- rep(1:45, 162/3)
+
+line  <- rep(c("wt", "rnt", "empty"), times=45*c(20, 20, 14))
+
+
+flour <- indata[, seq(3, 162, 3)]
+
+qpcr <- data.frame(flour= as.vector(as.matrix(flour[,c(1:7,seq(21,33,2))])),
+                   lines=factor(rep(c("wt", "rnt"), times=45*c(7, 7))),
+                   cycle=rep(1:45, 14),
+                   experiment=rep(1:14,times=rep(45,14)))
+

man/bees.Rd

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+\name{bees}
+\alias{bees}
+\docType{data}
+\title{
+Bee data. Number of different types of bees caught.}
+\description{
+Number of different types of bees caught in plates of different
+colours. There are four locations and within each location there are
+three replicates consisting of three plates of the three different
+colours (yellow, white and blue). Data are collected at 5 different
+dates over the summer season. Only data from one date available until
+data has been published.}
+\usage{data(bees)}
+\format{
+  A data frame with 72 observations on the following 7 variables.
+  \describe{
+    \item{\code{Locality}}{a factor with levels \code{Havreholm} \code{Kragevig} \code{Saltrup} \code{Svaerdborg}. Four different localities in Denmark.}
+    \item{\code{Replicate}}{a factor with levels \code{A} \code{B} \code{C}}
+    \item{\code{Color}}{a factor with levels \code{Blue} \code{White} \code{Yellow}. Colour of  plates}
+    \item{\code{Time}}{a factor with levels \code{july1} \code{july14}
+      \code{june17} \code{june3} \code{june6}. Data collected at
+      different dates in summer season. Only one day is present in the
+      current data frame until the full data has been released.}
+    \item{\code{Type}}{a factor with levels \code{Bumblebees} \code{Solitary}. Type of bee.}
+    \item{\code{Number}}{a numeric vector. The response variable with number of bees catched.}
+    \item{\code{id}}{a numeric vector. The id of the clusters (each containg three plates).}
+  }
+}
+%\details{
+%%  ~~ If necessary, more details than the __description__ above ~~
+%}
+\source{
+Data were kindly provided by Casper Ingerslev Henriksen, Department of
+Agricultural Sciences, KU-LIFE.
+Added by Torben Martinussen <tma@life.ku.dk>
+}
+%\references{
+%%  ~~ possibly secondary sources and usages ~~
+%}
+\examples{
+data(bees)
+model <- glm(Number ~ Locality + Type*Color,
+             family=poisson, data=bees)
+}
+\keyword{datasets}

man/clotting.Rd

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+\name{clotting}
+\alias{clotting}
+\docType{data}
+\title{Blood clotting for 158 rats}
+\description{
+Blood clotting activity (PCA) is measured for 158 Norway rats
+from two locations just before (baseline) and four days after injection of
+an anticoagulant (bromadiolone). Normally this would cause reduced
+blood clotting after 4 days compared to the baseline, but these rats are
+known to possess anticoagulent resistence to varying extent. The purpose
+is to relate anticoagulent resistence to gender and location and perhaps 
+weight. Dose of injection is, however, admistered according to weight and gender.
+}
+\usage{data(clotting)}
+\format{
+  A data frame with 158 observations on the following 6 variables.
+  \describe{
+    \item{\code{rat}}{a numeric vector}
+    \item{\code{locality}}{a factor with levels \code{Loc1} \code{Loc2}}
+    \item{\code{sex}}{a factor with levels \code{F} \code{M}}
+    \item{\code{weight}}{a numeric vector}
+    \item{\code{PCA0}}{a numeric vector with percent blood clotting activity at baseline}
+    \item{\code{PCA4}}{a numeric vector with percent blood clotting activity on day 4}
+  }
+}
+%\details{
+%%  ~~ If necessary, more details than the __description__ above ~~
+%}
+\source{
+Ann-Charlotte Heiberg, project at
+The Royal Veterinary and Agricultural University, 1999. \cr
+Added by Ib M. Skovgaard <ims@life.ku.dk>  
+}
+%\references{
+%}
+\examples{
+ data(clotting)
+ dim(clotting)
+ head(clotting)
+ day0= transform(clotting, day=0, pca=PCA0)
+ day4= transform(clotting, day=4, pca=PCA4)
+ day.both= rbind(day0,day4)
+ m1= lm(pca ~ rat + day*locality + day*sex, data=day.both)
+ anova(m1)
+ summary(m1)
+ m2= lm(pca ~ rat + day, data=day.both)
+ anova(m2)
+## Log transformation suggested.
+## Random effect of rat.
+## maybe str(clotting) ; plot(clotting) ...
+}
+\keyword{datasets}

man/greenland.Rd

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+\name{greenland}
+\alias{greenland}
+\docType{data}
+\title{
+Average yearly summer air temperature for Tasiilaq, Greenland
+}
+\description{
+Average yearly summer (June, July, August) air temperature for Tasiilaq, Greenland
+}
+\usage{data(greenland)}
+\format{
+  A data frame with 51 observations on the following 2 variables.
+  \describe{
+    \item{\code{year}}{year}
+    \item{\code{airtemp}}{average air temperature (degrees Celcius)}
+  }
+}
+%\details{
+%%  ~~ If necessary, more details than the __description__ above ~~
+%}
+\source{
+  Data provided by Sebastian Mernild.\cr
+  Originally obtained from http://www.dmi.dk/dmi/index/gronland/vejrarkiv-gl.htm. \cr
+  Added by Claus Ekstrom <ekstrom@life.ku.dk>  
+}
+\references{
+  Aktuelt Naturvidenskab september 2010. \cr
+  http://aktuelnaturvidenskab.dk/fileadmin/an/nr-4/an4_2010gletscher.pdf    
+}
+\examples{
+data(greenland)
+model <- lm(airtemp ~ year, data=greenland)
+plot(greenland$year, greenland$airtemp, xlab="Year", ylab="Air temperature")
+abline(model, col="red")
+}
+\keyword{datasets}

man/qpcr.Rd

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+\name{qpcr}
+\alias{qpcr}
+\docType{data}
+\title{Gene expression from real-time quantitative PCR}
+\description{
+  Gene expression levels from real-time quantitative polymerase chain
+  reaction (qPCR) experiments on two different plant lines. Each line was used
+  for 7 experiments each with 45 cycles. 
+}
+\usage{data(qpcr)}
+\format{
+  A data frame with 630 observations on the following 4 variables.
+\tabular{lll}{
+\code{flour}     \tab numeric \tab Fluorescence level\cr
+\code{line}      \tab factor  \tab Plant lines \code{rnt} (mutant) and \code{wt} (wildtype)\cr
+\code{cycle}     \tab numeric \tab Cycle number for the experiment\cr
+\code{transcript}\tab factor  \tab Transcript used for the different runs\cr
+       }
+
+%  \describe{
+%    \item{\code{flour}}{numeric Fluorescence level}
+%    \item{\code{lines}}{factor Plant lines \code{rnt}
+%    (mutant) and \code{wt} (wildtype)}
+%    \item{\code{cycle}}{numeric Cycle number for the experiment}
+%    \item{\code{experiment}}{numeric Experiment number}
+%  }
+}
+%\details{
+%%  ~~ If necessary, more details than the __description__ above ~~
+%}
+\source{
+Data provided by Kirsten Jorgensen <kij@life.ku.dk>. \cr
+Added by Claus Ekstrom <ekstrom@life.ku.dk>
+}
+\references{
+Morant, M. et al. (2010). Metabolomic, Transcriptional, Hormonal and
+Signaling Cross-Talk in Superroot2. \emph{Molecular Plant}. 3, p.192--211.  
+}
+\examples{
+data(qpcr)
+
+#
+# Analyze a single run for the wt line, transcript 1
+#
+run1 <- subset(qpcr, transcript==1 & line=="wt")
+
+model <- nls(flour ~ fmax/(1+exp(-(cycle-c)/b))+fb, 
+             start=list(c=25, b=1, fmax=100, fb=0), data=run1)
+
+print(model)
+
+plot(run1$cycle, run1$flour, xlab="Cycle", ylab="Fluorescence")
+lines(run1$cycle, predict(model))
+}
+\keyword{datasets}