1. Introduction to
2012-09-21 @HSPH
Kazuki Yoshida, M.D.
MPH-CLE student

2. Menu
n What is R?
n How does it compare to others?
n What are the advantages/disadvantages of R?
n Let’s install R.
n Editors and GUIs: How to make R more friendly

3. What is ?
http://www.r-project.org

4. is
a language and
environment for
statistical computing
and graphics
http://www.r-project.org/about.html

5. Menu
n What is R?
n How does it compare to others?
n What are the advantages/disadvantages of R?
n Let’s install R.
n Editors and GUIs: How to make R more friendly

6. Many statistical
packages

7. Software
SAS Stata JMP R SPSS
$65/yr
Cost (+Parallels& $179 Free for you None $55/yr
Windows)
Menus or Commands Menus (or
Mode of use Commands Menus
commands (or menus) commands)
Very Moderately Seasonal Rel. rare. Rare. More
Prevalence
prevalent prevalent cases in Incidence prevalent in
at HSPH
esp. in Epi esp in Bio June increasing? wild

8. Other packages
n CDC Epi Info: Field epidemiology
n TreeAgePro: Decision science
n SUDAAN: Survey data
n WinBUGS: Markov chain Monte Carlo
n Python: General-purpose programming language
n matlab, mathematica: Mathematics

9. Courses taught in R
n BIO 232 (Fall) Stat Methods I
n BIO 509 (Fall) Intro Stat Comp Environments
n BIO 503 (Winter) Program and Stat Model in R
http://isites.harvard.edu/icb/icb.do?keyword=k84377
n ID 271 (Spring) Adv Regression for Env Epi
n HMS BMI713.0 (Fall) Comp Stat for Biomed Sci
http://informaticstraining.hms.harvard.edu/content/lectures-and-problem-sets

10. Menu
n What is R?
n How does it compare to others?
n What are the advantages/disadvantages of R?
n Let’s install R.
n Editors and GUIs: How to make R more friendly

11. Advantages

12. is
Free as in
free beer
http://en.wikipedia.org/wiki/Free_Beer

13. is
Free as in
freedom
http://www.thefreedomtrail.org

14. People care about free
http://chereemoore.blogspot.com/2011/06/live-free-or-die.html

15. is
Developed by
Robert Gentleman Ross Ihaka
& user
community
Core Developer Team:
Douglas Bates, John Chambers, Peter Dalgaard, Seth Falcon, Robert Gentleman (Left), Kurt
Hornik, Stefano Iacus, Ross Ihaka (Right), Friedrich Leisch, Uwe Ligges, Thomas Lumley, Martin
Maechler, Duncan Murdoch, Paul Murrell, Martyn Plummer, Brian Ripley, Deepayan Sarkar,
Duncan Temple Lang, Luke Tierney, Simon Urbanek
http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html?pagewanted=all

16. 4000+
contributed
packages
Fast
development
http://r4stats.com/articles/popularity/

17. http://had.co.nz/ggplot2/
Flexible Graphics
http://www.stat.auckland.ac.nz/~paul/RG2e/ http://cran.r-project.org/web/packages/wordcloud/index.html

18. http://rpubs.com/kaz_yos/1285

19. pROC survival/rms
http://www.r-bloggers.com/u-s-unemployment-data-
animated-choropleth-maps/

20. Watch
additional
on-site demo

21. http://www.stat.auckland.ac.nz/~paul/
RG2e/chapter16.html
http://cran.r-project.org/web/packages/animation/index.html

22. Disadvantages

23. Learning
a new
L
language
is hard

24. R Commander: EZR:
http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ http://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/statmedEN.html
Lack of
standard
GUI
Deducer:
http://www.deducer.org/

25. NHANES3 dataset
Lack of
variable
labeling
Use memisc for partial fix

26. Not great for
big data (yet)
Use ff, bigmemory, etc
http://newscenter.berkeley.edu/2012/03/29/nsf-big-data-grant/

27. http://techreport.com/articles.x/15818
Single core
use
Turn on parallelization explicitly

28. Menu
n What is R?
n How does it compare to others?
n What are the advantages/disadvantages of R?
n Let’s install R.
n Editors and GUIs: How to make R more friendly

29. Let’s get
started!!

30. Download!!
http://www.r-project.org
http://rstudio.org

31. http://www.r-project.org

35. GUI toolkit

36. http://rstudio.org

37. OR

38. Install!!

39. Follow on-site
instruction

40. Menu
n What is R?
n How does it compare to others?
n What are the advantages/disadvantages of R?
n Let’s install R.
n Editors and GUIs: How to make R more friendly

41. Comparison of
environments

42. Standalone R.app
Fully functional Poor editor

43. RStudio editor
http://rstudio.org
Fully functional Not GUI

44. ESS on emacs editor
http://ess.r-project.org
Fully functional emacs is hard

45. Deducer GUI
http://www.deducer.org
Easy dialogues Very limited functionality

46. R Commander GUI
http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/
More functional Less sophisticated

47. EZR modification of R Commander GUI
http://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/
statmedEN.html
Focus on medical research Still in early development

49. For Your
Information

50. websites
n Download: http://www.r-project.org
n Look for packages: http://cran.r-project.org/web/
views/
n Look up abbreviations.: http://www.r-
bloggers.com/abbreviations-of-r-commands-
explained-250-r-abbreviations/
n Get up-to-date info: http://www.r-bloggers.com

51. editors
n RStudio: http://www.rstudio.org
n ESS for emacs: http://ess.r-project.org

52. GUI
n R Commander: http://socserv.mcmaster.ca/jfox/
Misc/Rcmdr/
n EZR: http://www.jichi.ac.jp/saitama-sct/
SaitamaHP.files/statmedEN.html
n Deducer: http://www.deducer.org/
n Rattle: http://rattle.togaware.com