Getting Started with R

What is R

  • R is

“a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc”

  • It has a ‘base’ system with thousands of additional packages
  • You need to install the base system, and then any further packages
  • The Comprehensive R Archive Network (CRAN) is at http://cran.r-project.org/index.html

Downloading R

  • From CRAN click on
    • Download R for windows
    • Install R for the first time
    • Download R 3.3.2 for Windows (or possibly Mac)
    • Both versions compatible
  • If using Windows
    • Right-click on the R icon to bring up properties
    • Add --internet2 to the end of the Target string on the Shortcut tab
    • Click on OK
  • Installing Rstudio
    • https://www.rstudio.com/products/rstudio/download/

R Basics

  • Inside R (most) data and results are stored in objects
  • Objects can be scalars, vectors, matrices, text strings, lists or more generic objects
  • Generic objects such as:
    • data frames
    • spatial objects similar to shapefiles
    • graphs
  • R is a programming language allowing new functions to be created
    • Some are already provided…

Vectors and Functions

heights <- c(4.7, 5.3, 6.2, 3.8, 4.4, 7.1, 2.5)
heights
## [1] 4.7 5.3 6.2 3.8 4.4 7.1 2.5
length(heights)
## [1] 7
sum(heights)
## [1] 34
mean(heights)
## [1] 4.857143
maxHeight <- max(heights)
maxHeight
## [1] 7.1

Subsets of Vectors - 1

heights
## [1] 4.7 5.3 6.2 3.8 4.4 7.1 2.5
heights[5]
## [1] 4.4
heights[3:6]
## [1] 6.2 3.8 4.4 7.1
heights[c(3,6,1)]
## [1] 6.2 7.1 4.7
heights[c(1,1,2,1,6)]
## [1] 4.7 4.7 5.3 4.7 7.1

Subsets of Vectors - 2

heights
## [1] 4.7 5.3 6.2 3.8 4.4 7.1 2.5
heights[c(-1,-4)]
## [1] 5.3 6.2 4.4 7.1 2.5
heights > 6
## [1] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE
which(heights > 6)
## [1] 3 6
heights[heights > 6]
## [1] 6.2 7.1

Testing conditions

if (heights[1] > 6) cat("Large\n") else cat("Small\n") 
## Small
# Can spread this over lines
if (heights[6] > 6) 
  cat("Large\n") else
  cat("Small\n")
## Large
# Can do multiple instructions
if (heights[1] < 6) {
  cat('Number is very small\n')
  cat('Here are all the heights in order',sort(heights))
}
## Number is very small
## Here are all the heights in order 2.5 3.8 4.4 4.7 5.3 6.2 7.1

Repetition - Loops 1

N <- length(heights)
for (i in 1:N) {
    if (heights[i] > 6) {
       cat(" Tree", i, "- tall.")
       } else {
       cat(" Tree", i, "- short.")
       }
  }
##  Tree 1 - short. Tree 2 - short. Tree 3 - tall. Tree 4 - short. Tree 5 - short. Tree 6 - tall. Tree 7 - short.

Determininistic loop - you know in advance how many cycles (N here)

Repetition - Loops 2

z <- 1
count <- 0
repeat {
  if (z > 100) break
  z <- z * 2
  count <- count + 1
  cat(z,' ')
}
## 2  4  8  16  32  64  128
cat('\n It took',count,' doubles to exceed 100.')
## 
##  It took 7  doubles to exceed 100.

Non-determininistic loop - you don’t know in advance how many cycles

Basic Types of Data

  • Sometimes called levels of measurement
  • Continuous (numerical)
    • ratio data (has a well defined zero) - eg height
    • interval data (no well defined zero) - eg date
  • Categorical (factor)
    • Ordinal data (rankable) - eg ‘strongly disagree’, … ,‘strongly agree’
    • Nominal data - (no intrinsic order) eg ‘red’, ‘blue’, ‘yellow’
  • Influences the type of analysis and visualisation

Factors in R

x <- c("MacOS","Linux","Windows","Windows","MacOS")
xf <- factor(x)
xf # Nominal
## [1] MacOS   Linux   Windows Windows MacOS  
## Levels: Linux MacOS Windows
y <- c("good","very good","good","average","poor","very poor","average")
yf <- factor(y,levels=c("very poor","poor","average","good","very good"),ordered=TRUE)
yf # Ordinal
## [1] good      very good good      average   poor      very poor average  
## Levels: very poor < poor < average < good < very good
yf[1] > y[3]
## [1] FALSE
xf[1] > xf[3]
## Warning in Ops.factor(xf[1], xf[3]): '>' not meaningful for factors

Graphics

  • R has a rich range of tools for visualising data
  • Visualisation is often an initial step in data exploration
  • Here are some simple examples - first a demonstration data set
head(mtcars,n=6)
##                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

mtcars is a built-in data frame: note that the columns are are different types: character, real, integer. We can use some simple exploratory visualisations…

Histogram

hist(mtcars$mpg,main="Fuel Consumption")

Boxplot

boxplot(mtcars$mpg,main="Fuel Consumption")

  • Shows median, quartiles, and the range

Boxplot: Comparing Categories

boxplot(mpg~cyl,main='Fuel Consumption',xlab='Cylinders',data=mtcars)

Boxplot: Nicer Horizontally

boxplot(mpg~cyl,main='Fuel Consumption',xlab='Cylinders',data=mtcars, horizontal=TRUE)

Note boxplot also finds outliers

Relationships: Scatterplot

plot(mtcars$wt,mtcars$mpg,main="MPG vs Weight")

Heavier cars have poorer fuel consumption

Space and Time Data

  • There is an equally rich variety of approaches for handling spatial and temporal data in R
  • These will be introduced over the next few weeks
  • Data sets
    • Rainfall records 1850 - 2014
    • Crime data