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R for Macroecology
Functions and plotting
A few words on for for( i in 1:10 )
A few words on for for( i in 1:10 )
1 2 3 4 5 6 7 8 910
A few words on for for( i in 1:10 )
1 2 3 4 5 6 7 8 910
i = 1Do any number of functions with iprint(i)x = sqrt(i)
A few words on for for( i in 1:10 )
1 2 3 4 5 6 7 8 910
i = 2Do any number of functions with iprint(i)x = sqrt(i)
A few words on for for( i in 1:10 )
1 2 3 4 5 6 7 8 910
i = 10Do any number of functions with iprint(i)x = sqrt(i)
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 =
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 = Y =
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 = Y =
1 2 3 4 5i = 1(so X[i] = 17)
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 = Y =
1 2 3 4 5i = 1(so X[i] = 17)
F
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 = Y =
1 2 3 4 5i = 2(so X[i] = 3)
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 = Y =
1 2 3 4 5i = 2(so X[i] = 3)
T
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 = Y = NA
1 2 3 4 5i = 2(so X[i] = 3)
8
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 = Y = NA
1 2 3 4 5
8 415
14
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 = 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
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
i j
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
1 NA
Y = NA NA
NA NA
i j
1 1
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
1 16
Y = 4 NA
NA NA
i j
112
121
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
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”)
Defining a functionSayHi = function(input)
{print(paste(“Hello”,input))}
SayHi(“Brody”)[1] “Hello Brody”
Defining a functionSayHi = function(input)
{print(paste(“Hello”,input))}
SayHi(“Brody”)[1] “Hello Brody”
SayHi()Error in paste("Hello", input) : argument "input" is missing, with no default
Defining a functionSayHi = function(input)
{print(paste(“Hello”,input))}
SayHi(“Brody”)[1] “Hello Brody”
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”)
{print(paste(“Hello”,input))}
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”
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