r for macroecology

R for Macroecology

Functions and plotting

A few words on for for( i in 1:10 )


1 2 3 4 5 6 7 8 910


1 2 3 4 5 6 7 8 910

i = 1Do any number of functions with iprint(i)x = sqrt(i)


1 2 3 4 5 6 7 8 910


i as an IndexX = c(17,3,-1,10,9)Y = NULLfor(i in 1:length(X))

{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X =


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y =


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y =

1 2 3 4 5i = 1(so X[i] = 17)


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y =

1 2 3 4 5i = 1(so X[i] = 17)

F


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y =

1 2 3 4 5i = 2(so X[i] = 3)


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y =

1 2 3 4 5i = 2(so X[i] = 3)

T


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y = NA

1 2 3 4 5i = 2(so X[i] = 3)

8


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y = NA

1 2 3 4 5

8 415

14


{if(X[i] < 12)

{Y[i] = X[i] + 5}

}

17

3 -110

9X = Y = NA

1 2 3 4 5

8 415

14

This vector (created by the for) indexes vectors X and Y

2-dimension equivalentX = matrix(1:6,ncol = 2,nrow = 3)Y = matrix(NA,ncol = 2,nrow = 3)

for(i in 1:nrow(X)){for(j in 1:ncol(X))

{Y[i,j] = X[i,j]^2}

}

1 4X = 2 5

3 6

NA NA

Y = NA NA

NA NA



{Y[i,j] = X[i,j]^2}

}

1 4X = 2 5

3 6

NA NA

Y = NA NA

NA NA

i j



{Y[i,j] = X[i,j]^2}

}

1 4X = 2 5

3 6

1 NA

Y = NA NA

NA NA

i j

1 1



{Y[i,j] = X[i,j]^2}

}

1 4X = 2 5

3 6

1 16

Y = 4 NA

NA NA

i j

112

121



{Y[i,j] = X[i,j]^2}

}

1 4X = 2 5

3 6

1 16

Y = 4 25

9 36

i j

112233

121212

Onward to today’s topics! Looking more at functions Plotting your data

Packages Sets of functions for a particular purpose

We will explore some of these in detail

install.packages()

require(package.name)

CRAN!

Function help

SyntaxArguments

Return

Function help

Writing your own functions Why bother?

We often have blocks of code that we want to execute many times, with small changes

Repetitive code is hard to read and likely to contain errors

Think about what variables the function should work on, and what the function should producemyFunction = function(argument, argument . . .)

{stuffmore stuffreturn(anObject)}

Defining a functionSayHi = function(input)

{print(paste(“Hello”,input))}

SayHi(“Brody”)



SayHi(“Brody”)[1] “Hello Brody”




SayHi()Error in paste("Hello", input) : argument "input" is missing, with no default




SayHi()Error in paste("Hello", input) : argument "input" is missing, with no default

Functions (usually) only have access to the variables given as arguments!

input = “Bob”SayHi()Error in paste("Hello", input) : argument "input" is missing, with no default

Defining a function with defaultsSayHi2 = function(input = “Sven”)


SayHi2(“Brody”)[1] “Hello Brody”

SayHi2()[1] “Hello Sven”

Things to remember about functions Use them whenever you have chunks of

repeated code

Remember to use return() to have the function return the desired object Not always necessary, sometimes you might just

want a function to plot something, or print something

Local/Global Functions only have access to variables passed as

arguments Changes to variables to and new variables defined

within the function are not available outside the function

A break to try things out

VectorFunctio

nNumbe

r

Value

Plotting For creating a plot

plot() hist()

For drawing on a plot points() segments() polygons()

For controlling how plots look par()

Make a new plotting window x11()

plot()x = 1:10y = 10:1plot(x,y)

plot()x = 1:10y = 10:1plot(x,y,main = “A plot”,xlab = “Temperature”,

ylab = “Pirates”)

type =

“l” “b” ”h”

“o” “s”

Plotting size and characters

cex = 2 or cex = 3

Plotting size and characters

pch = 10, cex = 3 pch = A, cex = 3 pch = A, cex = x

Color By name

“blue” or “dark grey” . . .

By function grey() rainbow() rgb()

Colorx = rep(1:10,10)y = rep(1:10,each=10)plot(x,y)

Colorx = rep(1:10,10)y = rep(1:10,each=10)plot(x,y,pch = 15,cex = 2)

Colorx = rep(1:10,10)y = rep(1:10,each=10)plot(x,y,pch = 15,cex = 2,col = “dark green”)

Colorx = rep(1:10,10)y = rep(1:10,each=10)plot(x,y,pch = 15,cex = 2,col = rgb(0.8,0.1,0.2))

Colorx = rep(1:10,10)y = rep(1:10,each=10)plot(x,y,pch = 15,cex = 2,col = rgb(seq(0,1,by = 0.01),0.1,0.2))

Drawing on plots points(x,y) adds points to existing plots

(with very similar options to plot()) segments(x0,y0,x1,y1) draws lines from

points to other points polygons()

The wonderful world of par() 70 different options to control your plots!

Plotting to a file pdf(), bmp() dev.off()

Some examples

All created entirely within R!

One last fun thing Scatterplots of massive data can be hard to

read

170265 data points

2-d histogram with hexagonal bins

Now the structure in the data is clearer

Hexagonal 2-d histograms hexbin() function in the package hexbin

Additional powerful plotting tools are found in the grid package, which provides a whole different approach to plotting

r for macroecology

Documents

indexes vectors x

y2dimension equivalentx

argument input

number of functions

datapackagessets of

macroecology r

blocks of code

small changesrepetitive