R language tutorial

1. David Chiu
R Language Tutorial
14/23/2013 Confidential | Copyright 2013 Trend Micro Inc.

2. Background of R
4/23/2013 2Confidential | Copyright 2012 Trend Micro Inc.

3. What is R?
• GNU Project Developed by John Chambers @ Bell Lab
• Free software environment for statistical computing and graphics
• Functional programming language written primarily in C, Fortran
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4. R Language
• R is functional programming language
• R is an interpreted language
• R is object oriented-language

5. Why Using R
• Statistic analysis on the fly
• Mathematical function and graphic module embedded
• FREE! & Open Source!
– http://cran.r-project.org/src/base/

6. Kaggle
http://www.kaggle.com/
R is the most widely language used by
kaggle participants

7. Data Scientist of these Companies Using R
What is your programming language of
choice, R, Python or something else?
“I use R, and occasionally matlab, for data analysis. There is
a large, active and extremely knowledgeable R community at
Google.”
http://simplystatistics.org/2013/02/15/interview-with-nick-chamandy-statistician-at-google/
4/23/2013 7Confidential | Copyright 2013 Trend Micro Inc.
“Expert knowledge of SAS (With Enterprise
Guide/Miner) required and candidates with
strong knowledge of R will be preferred”
http://www.kdnuggets.com/jobs/13/03-29-apple-sr-data-
scientist.html?utm_source=twitterfeed&utm_medium=facebook&utm_campaign=t
fb&utm_content=FaceBook&utm_term=analytics#.UVXibgXOpfc.facebook

8. Commercial support for R
• In 2007, Revolution Analytics providea commercial support for
Revolution R
– http://www.revolutionanalytics.com/products/revolution-r.php
– http://www.revolutionanalytics.com/why-revolution-r/which-r-is-right-for-me.php
• Big Data Appliance, which integrates R, Apache Hadoop, Oracle
Enterprise Linux, and a NoSQL database with the
Exadata hardware
– http://www.oracle.com/us/products/database/big-data-
appliance/overview/index.html

9. Revolotion R
• Free for Community Version
– http://www.revolutionanalytics.com/downloads/
– http://www.revolutionanalytics.com/why-revolution-r/benchmarks.php
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Base R 2.14.2
64
Revolution R
(1-core)
Revolution R
(4-core)
Speedup (4 core)
Matrix
Calculation
17.4 sec 2.9 sec 2.0 sec 7.9x
Matrix Functions 10.3 sec 2.0 sec 1.2 sec 7.8x
Program Control 2.7 sec 2.7 sec 2.7 sec Not Appreciable

10. IDE
R Studio
• http://www.rstudio.com/
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RGUI
• http://www.r-project.org/

11. Web App Development
Shiny makes it super simple for R users like you to turn
analyses into interactive web applications that anyone
can use
http://www.rstudio.com/shiny/
4/23/2013 11Confidential | Copyright 2013 Trend Micro Inc.

12. Package Management
• CRAN (Comprehensive R Archive Network)
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Repository URL
CRAN http://cran.r-project.org/web/packages/
Bioconductor http://www.bioconductor.org/packages/release/Software.html
R-Forge http://r-forge.r-project.org/

13. R Basic
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14. Basic Command
• help()
– help(demo)
• demo()
– demo(is.things)
• q()
• ls()
• rm()
– rm(x)
4/23/2013 14Confidential | Copyright 2013 Trend Micro Inc.

15. Basic Object
• Vector
• List
• Factor
• Array
• Matrix
• Data Frame
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16. Objects & Arithmetic
• Scalar
– x=3; y<-5; x+y
• Vectors
– x = c(1,2,3, 7); y= c(2,3,5,1); x+y; x*y; x – y; x/y;
– x =seq(1,10); y= 2:11; x+y
– x =seq(1,10,by=2); y =seq(1,10,length=2)
– rep(c(5,8), 3)
– x= c(1,2,3); length(x)
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17. Summaries and Subscripting
• Summary
– X = c(1,2,3,4,5,6,7,8,9,10)
– mean(x), min(x), median(x), max(x), var(x)
– summary(x)
• Subscripting
– x = c(1,2,3,4,5,6,7,8,9,10)
– x[1:3]; x[c(1,3,5)];
– x[c(1,3,5)] * 2 + x[c(2,2,2)]
– x[-(1:6)]
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18. Lists
• Contain a heterogeneous selection of objects
– e <- list(thing="hat", size="8.25"); e
– l <- list(a=1,b=2,c=3,d=4,e=5,f=6,g=7,h=8,i=9,j=10)
– l$j
– man = list(name="Qoo", height=183); man$name

19. Factor
• Ordered collection of items to present categorical value
• Different values that the factor can take are called levels
• Factors
– phone =
factor(c('iphone', 'htc', 'iphone', 'samsung', 'iphone', 'samsung'))
– levels(phone)
4/23/2013 19Confidential | Copyright 2013 Trend Micro Inc.

20. Matrices & Array
• Array
– An extension of a vector to more than two dimensions
– a <- array(c(1,2,3,4,5,6,7,8,9,10,11,12),dim=c(3,4))
• Matrices
– A vector to two dimensions – 2d-array
– x = c(1,2,3); y = c(4,5,6); rbind(x,y);cbind(x,y)
– x = rbind(c(1,2,3),c(4,5,6)); dim(x)
– x<-matrix(c(1,2,3,4,5,6),nr=3);
– x<-matrix(c(1,2,3,4,5,6),nrow=3, ,byrow=T)
– x<-matrix(c(1,2,3,4),nr=2);y<-matrix(c(5,6),nr=2); x%*%y
– t(matrix(c(1,2,3,4),nr=2))
– solve(matrix(c(1,2,3,4),nr=2))

21. Data Frame
• Useful way to represent tabular data
• essentially a matrix with named columns may also
include non-numerical variables
• Example
– df = data.frame(a=c(1,2,3,4,5),b=c(2,3,4,5,6));df

22. Function
• Function
– `%myop%` <- function(a, b) {2*a + 2*b}; 1 %myop% 1
– f <- function(x) {return(x^2 + 3)}
create.vector.of.ones <- function(n) {
return.vector <- NA;
for (i in 1:n) {
return.vector[i] <- 1;
} return.vector;
}
– create.vector.of.ones(3)
• Control Structures
– If …else…
– Repeat, for, while
• Catch error – trycatch

23. Anonymous Function
• Functional language Characteristic
– apply.to.three <- function(f) {f(3)}
– apply.to.three(function(x) {x * 7})

24. Objects and Classes
• All R code manipulates objects.
• Every object in R has a type
• In assignment statements, R will copy the object, not
just the reference to the object Attributes

25. S3 & S4 Object
• Many R functions were implemented using S3 methods
• In S version 4 (hence S4), formal classes and methods
were introduced that allowed
– Multiple arguments
– Abstract types
– inheritance.

26. OOP of S4
• S4 OOP Example
– setClass("Student", representation(name =
"character", score="numeric"))
– studenta = new ("Student", name="david", score=80 )
– studentb = new ("Student", name="andy", score=90 )
setMethod("show", signature("Student"),
function(object) {
cat(object@score+100)
})
– setGeneric("getscore", function(object)
standardGeneric("getscore"))
– Studenta

27. Packages
• A package is a related set of functions, help files, and
data files that have been bundled together.
• Basic Command
– library(rpart)
– CRAN
– Install
– (.packages())

28. Package used in Machine Learning for
Hackers
4/23/2013 28Confidential | Copyright 2013 Trend Micro Inc.

29. Apply
• Apply
– Returns a vector or array or list of values obtained by applying a
function to margins of an array or matrix.
– data <- cbind(c(1,2),c(3,4))
– data.rowsum <- apply(data,1,sum)
– data.colsum <- apply(data,2,sum)
– data
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30. Apply
• lapply
– returns a list of the same length as X, each element of which is
the result of applying FUN to the corresponding element of X.
• sapply
– is a user-friendly version and wrapper of lapply by default
returning a vector, matrix or
• vapply
– is similar to sapply, but has a pre-specified type of return
value, so it can be safer (and sometimes faster) to use.
4/23/2013 30Confidential | Copyright 2013 Trend Micro Inc.

31. File IO
• Save and Load
– x = USPersonalExpenditure
– save(x, file="~/test.RData")
– rm(x)
– load("~/test.RData")
– x

32. Charts and Graphics

33. Plotting Example
– xrange = range(as.numeric(colnames(USPersonalExpenditure)));
– yrange= range(USPersonalExpenditure);
– plot(xrange, yrange, type="n", xlab="Year",ylab="Category" )
– for(i in 1:5) {
lines(as.numeric(colnames(USPersonalExpenditure)),USPersonalExpenditur
e[i,], type="b", lwd=1.5)
}

34. IRIS Dataset
• data()

35. IRIS Dataset
• The Iris flower data set or Fisher's Iris data set is
a multivariate data set introduced by Sir Ronald
Fisher (1936) as an example ofdiscriminant analysis.[1] It
is sometimes called Anderson's Iris data set
– http://en.wikipedia.org/wiki/Iris_flower_data_set
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Iris setosa Iris versicolor Iris virginica

36. Classification of IRIS
• Classification Example
– install.packages("e1071")
– pairs(iris[1:4],main="Iris Data
(red=setosa,green=versicolor,blue=virginica)", pch=21,
bg=c("red","green3","blue")[unclass(iris$Species)])
– classifier<-naiveBayes(iris[,1:4], iris[,5])
– table(predict(classifier, iris[,-5]), iris[,5])
– classifier<-svm(iris[,1:4], iris[,5]) > table(predict(classifier, iris[,-
5]), iris[,5] + )
– prediction = predict(classifier, iris[,1:4])
• http://en.wikibooks.org/wiki/Data_Mining_Algorithms_In_R/Classification/Na%C3%A
Fve_Bayes
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37. Performance Tips
• Use Built-in Math Functions
• Use Environments for Lookup Tables
• Use a Database to Query Large Data Sets
• Preallocate Memory
• Monitor How Much Memory You Are Using
• Cleaning Up Objects
• Functions for Big Data Sets
• Parallel Computation with R

38. R for Machine Learning
4/23/2013 38Confidential | Copyright 2012 Trend Micro Inc.

39. Helps of the Topic
• ?read.delim
– # Access a function's help file
• ??base::delim
– # Search for 'delim' in all help files for functions in 'base'
• help.search("delimited")
– # Search for 'delimited' in all help files
• RSiteSearch("parsing text")
– # Search for the term 'parsing text' on the R site.

40. Sample Code of Chapter 1
• https://github.com/johnmyleswhite/ML_for_Hackers.git
4/23/2013 40Confidential | Copyright 2013 Trend Micro Inc.

41. Reference & Resource
4/23/2013 41Confidential | Copyright 2012 Trend Micro Inc.

42. Study Material
• R in a nutshell
4/23/2013 42Confidential | Copyright 2013 Trend Micro Inc.

43. Online Reference
4/23/2013 43Confidential | Copyright 2013 Trend Micro Inc.

44. Community Resources for R help
4/23/2013 44Confidential | Copyright 2013 Trend Micro Inc.

45. Resource
• Websites
– Stackoverflow
– Cross Validated
– R-help
– R-devel
– R-sig-*
– Package-specific mailing list
• Blog
– R-bloggers
• Twitter
– https://twitter.com/#rstats
• Quora
– http://www.quora.com/R-software
4/23/2013 45Confidential | Copyright 2013 Trend Micro Inc.

46. Resource (Con’d)
• Conference
– useR!
– R in Finance
– R in Insurance
– Others
– Joint Statistical Meetings
– Royal Statistical Society Conference
• Local User Group
– http://blog.revolutionanalytics.com/local-r-groups.html
• Taiwan R User Group
– http://www.facebook.com/Tw.R.User
– http://www.meetup.com/Taiwan-R/
4/23/2013 46Confidential | Copyright 2013 Trend Micro Inc.

47. Thank You!
4/23/2013 47Confidential | Copyright 2012 Trend Micro Inc.