Rexamples.Rnw

%\VignetteIndexEntry{Analysis of bead-summary data}
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% library('knitr'); rm(list=ls()); knit('beadsummary.Rnw')

\documentclass[12pt]{article}
\newcommand{\usecase}{\textit{\textbf{Use Case: }}}

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\usepackage{ifthen} 
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\newcommand{\ifinclude}[1]{\ifthenelse{\boolean{includethis}}{#1}{}} 



\title{Reading and exploring data using R - Examples}
\author{Mark Dunning}
\begin{document}
\maketitle
\tableofcontents

\section{UK Birth Rates}

These data were obtained from \href{http://www.theguardian.com/news/datablog/2011/jun/08/life-expectancy-uk-data-health}{a Guardian blog of June 2011}

\subsection{Reading the data}

We will read the file into R. As a rule-of-thumb, if the extension of the file is \textit{.tsv}, then the \Rfunction{read.delim} function can be used. Assuming that the file is read without error, we should print the first few lines of the file using \Rfunction{head} to check that the contents are as we expect. We can also check the dimensions of the data frame that we have created.

<<>>=

birth <- read.delim("data/UKBirthRate.tsv")
head(birth)
dim(birth)
summary(birth)
str(birth)
@

\subsection{Visualisation}

Lets assume that we want to visualise

<<>>=
plot(birth[,1],birth[,2])

@

\subsubsection{Changing the plot character}

<<>>=
plot(birth[,1],birth[,2],pch=16)
@


\subsubsection{Changing the plot type}

<<>>=
plot(birth[,1],birth[,2],type="l")

@


\subsubsection{Adding colours}

A complete list of colours can be seen \href{http://www.stat.columbia.edu/\~tzheng/files/Rcolor.pdf}{here}

<<>>=
plot(birth[,1],birth[,2],type="l",col="steelblue")

@



\subsubsection{Modifying the labels and title}


<<>>=
plot(birth[,1],birth[,2],xlab="Year",ylab="Births",main="Male birth rate", type="l")
@

\subsubsection{Adding extra lines and points}

<<>>=
plot(birth[,1],birth[,2],xlab="Year",ylab="Births",type="l",col="steelblue")
lines(birth[,1],birth[,3],col="midnightblue")
@

\subsubsection{Adding a legend}

<<>>=
plot(birth[,1],birth[,2],xlab="Year",ylab="Births",type="l",col="steelblue")
lines(birth[,1],birth[,3],col="midnightblue")
legend("topleft", fill=c("steelblue", "midnightblue"),legend=c("Male", "Female"))

@

\subsubsection{Adding text and points}

<<>>=
plot(birth[,1],birth[,2],xlab="Year",ylab="Births",type="l",col="steelblue")
lines(birth[,1],birth[,3],col="midnightblue")
legend("topleft", fill=c("steelblue", "midnightblue"),legend=c("Male", "Female"))
events <- which(birth[,4] != "")

points(birth[events,1],birth[events,2],pch=16)
points(birth[events,1],birth[events,3],pch=16)
abline(v = birth[events,1])
text(birth[events,1], 80, birth[events,4],srt=45)
@


\subsection{Statistical analysis}



\section{Rail station usage}
These data were obtained from \href{http://www.theguardian.com/news/datablog/2009/jul/02/rail-transport-travelleisure}{a Guardian blog of July 2009}

<<>>=
stations <- read.csv("data/Station use - 2011-12.csv",stringsAsFactors=FALSE)
head(stations)
@

Suppose we are interested in which stations are most / least busy. A measure of this is given in the column 'X1112.Entries...Exits'. However, this is a bit messay so we will create a new variable with the same data. 
<<>>=
stations$Total <- stations$X1112.Entries...Exits
@

Now try and find the station with the most exits and entrances using the \Rfunction{max} and \Rfunction{which.max}. Does the answer look correct to you? What has gone wrong?

<<>>=
max(stations$Total)
@

The problem arises because the numbers in the original file had comma separators in them. 
<<>>=
stations$Total <- as.numeric(gsub(",", "",stations$Total))

max(stations$Total)
stations[which.max(stations$Total),]
@




\end{document}