Introduction to R - Functions, Packages

1
Introduction to R - Functions, Packages

• Andrew Jaffe
• 10/18/10

2
Overview

• Functions
• Packages
• Questions

3
Functions

• Everything you use in R is a built-in function
• You can download new functions (packages next
  section)
• You can add your own to a script

4
Functions

• Built in functions (note the lack of parenthesis
  this is also why you dont want to name
  variables as functions)

gt rep function (x, ...) .Primitive("rep") gt
c function (..., recursive FALSE)
.Primitive("c")
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Functions

• Syntax functionName lt- function(inputs) body
  of the function which returns something
• You must run/submit the function before you can
  use it
• Note that variable naming within a function is
  protected, and not altered by whatever your
  script is doing

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Functions
Input
tests if a number if positive pos function(x)
if(x gt 0) out 1 if(x lt 0) out
0 return(out)
Output
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Functions
gt pos function(x) if(x gt 0) out 1 if(x
lt 0) out 0 return(out) gt pos(5) 1 1 gt
pos(-5) 1 0
Run the function first
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Functions

• The value that the function returns can be stored
  as a new variable

gt y pos(4) gt y 1 1
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Functions
gt protected x is the input to pos gt x
3 gt pos(6) 1 1 gt x 1 3
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Functions

• Using return() explicitly tells the function what
  to return safe
• Otherwise, the function will return the last
  value that it works with or assigns
• This can be an issue if you use a lot of logical
  statements

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Functions

• Adding a verbose logical variable gives the
  user some feedback

gt pos function(x,verboseTRUE) if(x gt 0)
out 1 if(x lt 0) out 0 if(verbose)
cat("finished running","\n") return(out) gt
y pos(5) finished running gt y 1 1
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Functions

• You can change the input into functions when you
  run them
• You can name each input, or just put their values
  in order

gt y pos(5, verbose FALSE) gt y pos(5, FALSE)
same thing gt y 1 1
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Functions

• Here, we set verbose to be TRUE by default, ie
  that that function says what its doing
• Using verbose statements throughout your
  functions makes it easier to use (especially if
  other people are going to use your function)

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Functions

• Note really long for loops also benefit from
  using verbose statements
• mod, the remainder of the first number
  divided by the second
• Print a period every 10,000 iterations

for(i in 11e5) if(i 10000 0)
cat(".") do other stuff
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Functions

• Why do functions?
• Provides modularity to your code
• You can solve small problems using functions
• Keeps your actual analysis script cleaner
• You can distribute your code script to other
  people

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Functions

• For example, download the lecture notes, and type
  source(lecture_notes.R)
• The pos function should be added into your
  working directory
• Another function, mypar was added, but requires
  a package!

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Functions

• Make a function that takes two numbers as inputs,
  and returns their sum
• Make a function that takes three inputs as inputs
  and returns their product

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Functions
summ lt- function(a,b) out ab return(out)
prodd lt- function(a,b,c) out
abc return(out)
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Overview

• Functions
• Packages
• Questions

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Packages

• R can access and install a huge library of
  packages
• The full list is here http//cran.r-project.org/w
  eb/packages/
• You only need to install a package once, then you
  can use it whenever you want

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Packages

• ?install.packages
• Lets try downloading RColorBrewer
• install.packages(RColorBrewer)
• A list of repository directories should pop-up ?
  select USA (basically any of them will work)
• I think the Maryland one is Hopkins

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Packages

• Some installation popups occurs and the package
  should be installed on your computer
• Then, library(package_name)
• library(RColorBrewer) quotes are optional

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Packages

• ?RColorBrewer Creates nice looking color
  palettes especially for thematic maps
• Top left corner RColorBrewer RColorBrewer
• Top left in mean mean base
• The thing in is the package

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Packages

• Now, resource the lecture 7 notes so that the
  mypar() function gets read in correctly
• This function will alter the plot parameters to
  make the color palette more divergent, changes
  the margin sizes, and can allow you to plot
  multi-panel plots

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Packages

• mypar() default is 1 x 1 plot space
• mypar(2,2) 2 rows, 2 columns

gt data(cars) gt mypar() gt plot(cars, type "b",
col 5)
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Packages

• I usually google R something Im trying to
  do and sometimes links can direct you to
  existing packages
• The full list is on the CRAN website
• Some Epi ones are survival survival analysis,
  lme4 longitudinal data analysis, Epi some
  epi functions

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Packages

• Try installing those packages now
• Remember, to use a package, you must invoke the
  library(package) command

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Packages

• library(survival)
• ?survival
• ??survival fuzzy search
• ?Surv

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Overview

• Functions
• Packages
• Questions

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Questions?

• Any burning R questions? Open floor