A Crash Course in R

This code has been kindly contributed by Robin Edwards (from UCL CASA).

There are many useful introductory guides out there to R, but below is the kind of thing I now wish I’d been given when I first started using it – something with simple logically-progressive examples and minimal explanatory text. Copy the text below into a new script in R and run line-by-line to give a quick intro to many of R’s most basic principles and functionality. You can also download a text file with it here. It is by no means comprehensive, even at the most basic level, but still I hope someone finds it useful. You may want to look at RStudio as it is more user-friendly. ## A CRASH COURSE IN [R] PROGRAMMING ## Robin Edwards (geotheory.co.uk), March 2013 ## In RStudio run through line-by-line using Ctrl + Enter

# basic R environmental functions x=3.14159; y=’hello world’; z=TRUE # create some objects. In RStudio they’ll appear in ‘Workspace’ ls() # list the objects in the Workspace print(y) # print information to R ‘Console’ rm(y) # remove an object rm(list=ls()) # remove all getwd() # find current working directory setwd(“/Users/robinedwards/Documents”) # set working directory as preferred print ( “R ignores the ‘white-space’ in command syntax” )

# use ‘?’ for help on any R function (if its library is loaded in the session) ?max ??csv # search for a text string in R documentation library library(help=utils) # get help on a particular package (list its functions)

# ‘str’ is a powerful tool for investigating the underlying structure of any R object str(max)

# CREATING AND MANIPULATING R OBJECTS

# assigning values to variables n = 5 # is possible but n 5 -> n rm(n)

# R objects can be of various data types, but probably most common are ‘numeric’ and ‘character’ ( num ( char <- ‘any text string’ )

# create a VECTOR (array) using the ‘c()’ concatenate function ( vec

# a vector series ( vec

# R vectors can be accessed in various ways using [ ] brackets vec[3] vec[3:6] vec[ c(1,3,8) ] vec[vec > 15]

# check a vector contains a value 5 %in% vec 12 %in% vec

# finding first index position of a matching value/sting ( x = c(‘one’, ‘five’, ‘two’, 3, ‘two’) ) match(‘two’, x) match(c(‘two’,'five’), x)

# a MATRIX is a 2D vector (essentially a vector of vectors) of matching data type ( matrx = matrix(1:15, 3, 5) ) ( matrx dim(matrx) print(matrx) t(matrx) # a matrix can be easily transposed

# an ARRAY is a generic vector but with more flexibiity. A 1D array is the same as a normal vector, # and a 2D array is like a matrix. But arrays can store data with ‘n’ dimensions: ( arry

# Using square brackets on arrays arry[12] # a single criterion (argument) selects the array’s n’th record arry[3,1,2] # or use multiple arguments that reflect the array’s dimensionality arry[,,2] arry[,1,]

# a DATA.FRAME is like a matrix, but accomodates fields (columns) with different data types (df

# They can be viewed easily View(df)

# examine their internal stucture str(df)

# data interrogation with square brackets df[1,] df[2:3,] df[,1] df[2,1]

# data.frame and matrix objects can have field (column) and record (row) names dimnames(df) colnames(df) names(df) # not for matrix objects row.names(df)

# interrogate data.frames by field name using the ‘$’ operator. the result is a simple vector df$name df$name[2]

# names can be reassigned names(df) row.names(df) print(df)

# check dimensions of vector/matrix/array/data.frame objects length(vec) dim(df) dim(arry) nrow(df) ncol(df)

# R has various inbuilt data.frame datasets used to illustrate how functions operate e.g. data() InsectSprays # this guide makes use of these datasets warpbreaks

# examine contents head(InsectSprays) # list the top records of a vector / matrix / d.f. tail(InsectSprays, n=3) # bottom the 3 summary(InsectSprays) # summarise a data vector

# aggregate() is a powerful function for summarising categorical data aggregate(InsectSprays$count, by=list(InsectSprays$spray), FUN=mean) sumInsects names(sumInsects) print(sumInsects)

# subset/apply filter to a data.frame warpbreaks[warpbreaks$wool=='A',] # by 1 condition warpbreaks[warpbreaks$tension %in% c('L','M'),] # multiple conditions

# adding entries is possible (if a bit tricky) (newrow (warpbreaks

# but LISTS are better at this lst = list()

# ways to assign/add items lst[1] = “one” lst[[2]] <- “two” lst[length(lst)+1] <- “three” print(lst)

# data retrieval lst[[1]] # double brackets means the object returned is of the data class of the list item lst[2:3] # selecting a more than 1 list item is possible with single brackets.. lst[c language="(1,3)"][/c] # but the object returned (from single bracket interrogation) is a list

# delete list items lst[[3]] lst[1:2] lst

# entries can be any object type (like python), including other lists (double bracketting) lst[[1]] lst[[2]] <- ‘item2′ lst lst[[1]][[1]]

# Data in lists can also be stored and recalled by key word/number (like Python’s dictionary class) dict dict['wed'] print(dict) dict[['tues']] dict[c language="('mon','wed')"][/c]

# reorder a vector with ‘sort’ vec sort(vec)

# or a dataframe with ‘order’ df[order(df$years),]

# LOGICAL objects (booleans) are binary true/false objects that facilitate conditional data processing (bool (bool

# query an object’s data/structure type with ‘class()’ class(bool) class(num) # numeric is the default data type for number objects class(as.integer(num)) # integer class exists but is not default class(char) # character class class(’237′ ) # numbers aren’t always numeric type as.numeric(’237′) # but can be converted as.character(237) # and vice verse

# Child-objects are often of different class to parents class(df) class(df[,2]) class(df[,1])

# FACTOR objects are vectors of items that have been categorised by unique values factr str(factr) levels(factr) table(factr)

# you may encounter problems converting a factor of numeric data to numeric type as.numeric(factr)

# instead do this as.numeric(as.character(factr))

# editing factors can be tricky print(df) df$person[1] <- ‘Matthew’

# instead convert to character or numeric etc df$person df$person[1] <- ‘Matthew’ df$person levels(df$person)

# LOGICAL OPERATIONS 2 + 2 == 4 # ‘==’ denotes value equality 3 <= 2 # less than or equal to 3 >= 2 # greater than or equal to ‘string’ == “string” ‘b’ >= ‘a’ # strings can be ranked 3 != 3 # NOT operator c(4,2,6) == c(4,2,8) # vector comparisons return locical vectors TRUE == T # ‘T’ and ‘F’ default as boolean shortcuts (until overwritten) TRUE & TRUE # AND operator TRUE | FALSE # OR operator F | F

# IF/ELSE statement (used in most logical procedures) x if(x < 5){ print(‘x is less than 5′) } else{ print(‘x is not less than 5′) }

if(T|F) print(‘single liners can dispense with curly brackets’) if(T&F) print(”) else print(“but then ‘else’ only works on the same line”)

# LOOPING FUNCTIONS – very useful for handling repetitive operations

# ‘FOR’ loop for(i in 1:10){ print(paste(‘number ‘,i)) }

# WHILE loop (be careful to include safeguards to prevent infinite loops) i = 30 while(i > 0){ print(paste(‘number ‘,i)) i = i – 3 }

# creating a function multiply tot return(tot) }

multiply(3,5) # note ‘tot’ wasn’t remembered outside the function – functions are contained environments # if required use ‘<<-’ for global assignment but be careful not to overwrite R’s internal objects # its generally better to do this: newVar

# handling ‘NA’ values (x = 1:5) x[8] = 8 x[3] = NA print(x) # sometimes functions will fail because of NA values na.omit(x) # iterates full list but ignores NAs x[na.omit(x)] is.na(x) # alternatively x[!is.na(x)]

# useful basic math functions seq(-2, 2, by=.2) # sequence of equal difference seq(length=10, from=-5, by=.2) # with range defined by vector length rnorm(20, mean = 0, sd = 1) # random normal distribution runif(20, min=0, max=100) # array of random numbers sample(0:100, 20, replace=TRUE) # array of random integers table(warpbreaks[,2:3]) # array summary stats (powerful summary tool) min(vec) max(vec) range(vec) mean(vec) median(vec) sum(vec) prod(vec) abs(-5) # magnitude sd(rnorm(10)) # standard deviation 4^2 # square sqrt(16) # square root 5%%3 # modulo (remainder after subtraction of any multiple) 6%%2 for(i in 1:100) if(i%%20==0) print(i) # useful for running an operation every n’th cycle

# Importing and exporting data using comma-separated file write.csv(df, ‘example.csv’) # save to csv file rm(df) (df

# PLOTTING IN R

# some basic functionality plot(1:10) plot(sort(rnorm(100)), pch=16, cex=0.5) # specifying point and size respectively plot(x=1:25, y=25:1, pch=1:25) # x & y inputs, and showing the available point symbols plot(sin, -pi, 2*pi) hist(rnorm(1000), breaks=50) barplot(sumInsects$sum, names.arg = sumInsects$group) pie(sumInsects$sum, labels = sumInsects$group)

# plots with more visual components are built up incrementally x plot(x, pch=17) lines(x, col=’#00FF00′) points(x+5, pch=16, col=’red’)

# stacking charts warpbreaks sumWB names(sumWB) sumWB (data barplot(data, names.arg=c(‘Group A’,'Group B’), legend.text=c(‘L’,'M’,'H’), args.legend = list(x = “right”))

barplot(data, names.arg=c(‘Group A’,'Group B’), beside=T, legend.text=c(‘L’,'M’,'H’), args.legend = list(x = “topright”))

# ‘symbols()’ is a good way to represent a 3rd data dimension (use square root for area proportionality) (cities lon=c(-0.1,-2.6,-2.2,-1.5), lat=c(51.5,51.4,53.5,53.8), pop=c(8,1,2.7,0.8))) symbols(x=cities$lon, y=cities$lat, circles=sqrt(cities$pop), inches=0.3, bg=’red’, fg=NULL, asp=T, xlab=’Longitude’, ylab=’Latitude’) abline(h=(seq(51,53,1)), col=”lightgray”, lty=1) abline(v=(seq(-4,1,1)), col=”lightgray”, lty=1) text(x=cities$lon, y=cities$lat+0.2, labels=cities$city)

# But for much easier and more elegant data visualisation use GGPLOT2

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