Introduction to R Lecture 1: Getting Started

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Introduction to RLecture 1 Getting Started

• Andrew Jaffe
• 8/30/10

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator

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About the Course

• Series of 7 seminars
• Covers the usage of R
• Platform for beginning analyses
• NOT covering statistics
• Good programming etiquette
• Bring your laptop there will be breaks to allow
  you to practice the code

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About the Course

• This seminar is 1 unit pass/fail
• To pass, attend 5 out of 7 seminars
• Very little outside work

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About the Course

• Some learning objectives include
• Importing/exporting data
• Data management
• Performing calculations
• Recoding variables
• Producing graphics
• Installing packages
• Writing functions

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About the Course

• Course communication via E-mail
• Lectures and code will be hosted on my webpage
• http//www.biostat.jhsph.edu/ajaffe/rseminar.html
  

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About the Instructor

• 3rd year PhD student in Genetic Epi program,
  concurrent MHS in Bioinformatics
• Learned R five years ago, been using regularly
  the last two

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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What is R?

• R is a language and environment for statistical
  computing and graphics
• R is the open source implementation of the S
  language, which was developed by Bell
  laboratories
• R is both open source and open development

http//www.r-project.org/
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What is R?

• Pros
• Free
• Tons of packages, very flexible
• Multiple datasets at any given time
• Cons
• Much more programming oriented
• Minimal interface

These are my personal opinions
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What is R?

• Often times, a good first step for data cleaning
  and manipulation
• Then, export data to STATA or SAS for Epi analyses

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What is R?
Console
Script
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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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Installing R

• http//cran.r-project.org/

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Installing R - Windows

• Windows click base and download

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Installing R - Windows

• Click the link to the latest build

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Installing R - Mac

• Mac click the latest packages .pkg file

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Installing R

• Double click the downloaded file
• Hit next a few times
• Use default settings
• Finish installing

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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Installing a Text Editor

• Windows Rs built-in text editor is terrible
• Its essentially Windows notepad
• We will download a much better one
• Mac Rs built-in text editor is sufficient
• Color coding, signals parenthesis closing, etc
• I suggest using this until you think you need a
  better one

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Installing a Text Editor

• I prefer Notepad
• http//notepad-plus-plus.org/
• Download the current version http//download.tuxf
  amily.org/notepadplus/5.7/npp.5.7.Installer.exe
• Install on your computer using defaults

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Installing a Text Editor
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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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Interfacing with R

• Scripts documents that contain reproducible R
  code and functions that you can send to the
  console (and save)
• Files are designated with the .R extension
• You can source scripts (more later)
• Console Type commands directly into the console
• Good for looking at your data, trying things, and
  plotting

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Interfacing with R - Mac

• Mac File ? New Script
• This opens the default text editor
• To send a line of code to the R console, press
  AppleEnter when the cursor is anywhere on that
  line
• Highlight chunks of code and press AppleEnter to
  send

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Interfacing with R - Windows

• Using the default text editor, pressing CtrlR
  sends lines to the console
• However, we want to use Notepad
• We need to download one more thing

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Interfacing with R - Windows

• NppToR Notepad to R
• http//sourceforge.net/projects/npptor/
• It must be running when R and Notepad are open
• When properly configured, press F8 to send lines
  of code, or highlighted chunks, to the console
• I will help configure this after class today

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Interfacing with R Windows

• More detailed instructions for installing NppToR
• http//sourceforge.net/apps/mediawiki/npptor/index
  .php?titleInstalling

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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Writing Scripts

• The comment symbol is (pound) in R
• Comment liberally - you should be able to
  understand a script after not seeing it for 6
  months
• Lines of s are useful to separate sections
• Useful for designating headers

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Writing Scripts

• Title Demo R Script
• Author Andrew Jaffe
• Date 7/30/10
• Purpose Demonstrate comments in R
• this is a comment, nothing to the right of it
  gets read
• this is still a comment you can use many
  s as you want
• sometimes you have a really long comment, like
  explaining what you
• are doing for a step in analysis. Take it to
  a second line

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Writing Scripts

• Some common etiquette
• You can use spaces (more generally white space)
  within functions and commands liberally as well
• Try to keep a reasonable number of characters per
  column many commands can be broken into
  multiple lines
• More to come later

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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R as a Calculator

• The R console functions as full calculator
• Try to play around with it
• , -, /, are add, subtract, multiply, and
  divide
• or is power
• ( and ) work with order of operations

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Lecture 1

• Course overview
• What is R?
• Installing R
• Installing a text editor
• Interfacing text editor with R
• Writing scripts
• Using R as a calculator
• Assignment

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Assignment

• The assignment operator assigning a value to a
  name
• R accepts two operators lt- and
• Ie x8 (remember whitespace! x 8, x lt- 8)
• Variable names are case-sensitive
• Ie X and x are different
• Set x 8, and try using calculator functions on x

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Assignment

• Assignment literally puts whatever is on the
  right side of the operator into your left-hand
  side variable
• Note that although you can name variables
  anything, you might run into some issues naming
  things the same as default R functions ? Np
  turns functions red/pink so you know

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Examples of assignment, introducing R data

• Enough to get R up and running if this is the
  only class you attend. We will see them in much
  more detail over the next three sessions

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Assignment

• status lt- c(case,case,case,
  control,control,control)
• status
• class(status)
• table(status)
• factor(status)
• alternatively status lt- c(rep(case,3),
  rep(control,3))

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Assignment

• web lt- http//www.biostat.jhsph.edu/ajaffe/code/
  lec1_code.R
• class(web)
• source(web)
• You also dont have to save tables/data you find
  online to your disk (note read.table works for
  most things below arent tables though)
• scan(web, whatcharacter(0), sep "\n")
• scan(http//www.google.com, whatcharacter(0))

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Assignment

• mat lt- matrix(c(1,2,3,4), nrow 2, ncol 2,
  byrow T) this is sourced in
• class(mat)
• mat
• mat mat
• mat mat
• mat mat

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Assignment

• class(dat) dat is also sourced in
• head(dat)
• table(datsex, datstatus)
• To be continued

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Questions?