revision.Rnw

<<knitr, echo=FALSE>>=
opts_chunk$set(tidy.opts = 
               list(width.cutoff = 50, 
                    tidy = FALSE),
               fig.align = 'center',
               stop_on_error = 1L,
               comment = NA,
               prompt = TRUE)
options(width = 60)
@ 
  
\section{Revision of basic R}

\begin{frame}{Basic R functions (size reflects frequency of usage)}
\begin{center}
  \includegraphics[height=0.8\textheight, keepaspectratio=true]{./Figures/functionCloud.png}
\end{center}
\end{frame}

\begin{frame}[fragile]{Defining functions in R}
Simple function with 4 arguments:  
\begin{scriptsize} 
<<function-example, echo=TRUE>>=
# Function to calculate area of rectangle
area <- function(x1, y1, x2, y2){
  abs(x2-x1) * abs(y2-y1)
}
area(0, 0, 5, 5)
@ 
\end{scriptsize}

Special argument "..." for any:

\begin{scriptsize} 
<<function-example2, echo=TRUE>>=
# Plot with a message before the plot
plotMsg <- function(x, y, ...){
	cat("Plotting", length(x), "data points!\n")
	plot(x, y, ...)
}
@ 
\end{scriptsize}

\end{frame}

\begin{frame}[fragile]{Output of plotMsg()}
\begin{scriptsize}
\setkeys{Gin}{height=0.7\textheight,keepaspectratio=true}
<<label=plotmsg, echo=TRUE, tidy=FALSE>>=
plotMsg(1:10, 1:10, main="My plot")
@
\end{scriptsize}
\end{frame}

%%% Useful functions

\begin{frame}[fragile]{Useful R function 1/2}
	\begin{itemize}
	\item readLines() - reads raw lines of text from a file
	\item nchar() - gives number of characters in a string
\begin{scriptsize} 
<<echo=TRUE>>=
nchar("Some text")
@
\end{scriptsize}
	\item strsplit() - split a string by some separator
\begin{scriptsize} 
<<echo=TRUE>>=
strsplit("Some text", " ")
strsplit("Some text", "")
@
\end{scriptsize}
	\item unique() - unique elements of a vector
\begin{scriptsize} 
<<echo=TRUE>>=
unique(c(1, 1, 2, 2, 3))
unique(c("a", "b", "a"))
@
\end{scriptsize}

	\end{itemize}
\end{frame}

\begin{frame}[fragile]{Useful R function 2/2}
	\begin{itemize}
	\item \code{grep()} - find which elements of vector match regular expression
\begin{scriptsize} 
<<echo=TRUE>>=
grep("[AT]+", c("CGC", "TAT", "TATCATA"))
@
\end{scriptsize}

	\item \code{sub()} - replace matches to regular expression
\begin{scriptsize} 
<<echo=TRUE>>=
sub("[AT]+", "-", c("CGC", "TAT", "TATCATA")) 
@
\end{scriptsize}

	\item \code{chartr()} - translate a string by replacing individual characters
\begin{scriptsize} 
<<echo=TRUE>>=
chartr("TA", "AT", "TATCTA")
@
\end{scriptsize}

	\item \code{rev()} - reverse ordering in a vector
\begin{scriptsize} 
<<echo=TRUE>>=
rev(c("TAT", "ATT", "TTT"))
@
\end{scriptsize}

	\item \code{paste()} - concatenate variables into a string representation
\begin{scriptsize} 
<<echo=TRUE>>=
paste(c("A", "T", "A"), collapse="")
@
\end{scriptsize}

	\end{itemize}
\end{frame}


%%% Revision of R lists

\begin{frame}[fragile]{Lists in R}
List is a data structure that can hold a vector of any other variables.
\bigskip
\begin{scriptsize} 
<<lists,echo=TRUE>>=
x <- list(a=10, b="text")
x$a
x[["b"]]
x[[1]]
names(x)
@
%$
\end{scriptsize}
\end{frame}

%%% Everything is object

\begin{frame}[fragile]{Everything in R has a class}
Everything in R has a type - in object oriented programming called a \textbf{class}.
\small
\begin{scriptsize} 
<<everythingobj,echo=TRUE>>=
class(c(1, 2, 3))
class("Some text")
class(matrix(0, nrow=10, ncol=10))
class(plot)
class(table(1:4, 1:4))
@
\end{scriptsize}

\end{frame}

\begin{frame}{Recommended coding standards}
  \begin{block}{Coding standards}
    \begin{itemize}
    \item Use \texttt{<-} for assignment rather than \texttt{=}.
    \item Avoid long lines (80 characters).
    \item Use spaces for identation (2 or 4).
    \item No semi-colomns (unless you have several expression in a line).
    \item Start names with upper case for classes, lower for the rest.
    \item Use syntax highlighting
    \end{itemize}
  \end{block}
\end{frame}