1. Reading data
into
2012-09-28 @HSPH
Kazuki Yoshida, M.D.
MPH-CLE student
FREEDOM
TO(KNOW

2. Previously in this group
! Group Website: http://rpubs.com/kaz_yos/useR_at_HSPH
! Introduction to R

3. Menu
! What statistics is all about.
! Data-reading functions in R
! Installing packages
! Reading excel files
! Reading other files

4. http://mediacrushllc.com/2012/internet-statistics-2012/
is the study of the
collection, organization, analysis, interpretation,
and presentation of
data
http://en.wikipedia.org/wiki/Statistics

5. No data,
No life
No statistics

6. Loading data is
the first step
http://echrblog.blogspot.com/2011/04/statistics-on-states-with-systemic-or.html

7. Supported
! .RData (native): load()
! .csv: read.csv()
! .xls/.xlsx: library(gdata) or library(XLConnect)
! .sas7bdat: read.sas7bdat() via library(sas7bdat)
! .dta: read.dta via library(foreign)
! and more...
http://cran.r-project.org/doc/manuals/R-data.html

8. library()
packages

9. 4000+
user-
contributed
packages
Fast
development
http://r4stats.com/articles/popularity/

10. Downside:
not much can be
done without
packages

11. CRAN

12. Comprehensive
R
Archive
Network
http://cran.r-project.org/web/packages/
available_packages_by_date.html

13. Let’s try

14. Open
R Studio

15. http://rstudio.org
Watch the screencast

16. Plot Workspace
switched
Console Source

17. Menu: RStudio - Preferences My configuration
Plot Workspace
Console Source

18. Menu: RStudio - Preferences My configuration
Configure CRAN mirror

19. Comma Separated Values
Use .CSV
if possible
http://www.edrugsearch.com/edsblog/cvs-takes-on-wal-marts-generic-drug-prices-with-a-gimmicky-twist/#.UEfft0J8z0d

20. .csv
http://www.wondergraphs.com/img/SFO_Landings.csv

21. read.csv(“file.csv”)
http://www.wondergraphs.com/img/SFO_Landings.csv
Careful big file!

22. name of a dataset here
new.dat <-
read.csv(“file.csv”)
file name here
function to read .csv files

23. alternatively
name of a dataset here
new.dat <-
read.csv(file.choose())
function to open a
function to read .csv files file-choose dialogue

24. Space separated
http://www.biostat.harvard.edu/~fitzmaur/ala2e/tlc.dat

25. read.table(“file.dat”)
or
read.table(“file.dat”, header = T)
http://www.biostat.harvard.edu/~fitzmaur/ala2e/tlc.dat

26. tab-separated

27. read.delim(“file.tsv”)
http://www.brookscole.com/cgi-wadsworth/
course_products_wp.pl?
fid=M20b&flag=student&product_isbn_issn=9780495384
960&disciplinenumber=1038&template=AUS

28. For comma-, tab-, or
space-separated text
Let’s try!

29. Excel files
prevalent
http://www.biography.com/people/bill-gates-9307520
http://www.last.fm/music/Excel/+images/285200

30. http://www.philipcoppens.com/matrixconstructs.html
We will use
publicly available
data
http://www.hsph.harvard.edu/faculty/miguel-
hernan/files/nhefs_book.xls
http://www.hsph.harvard.edu/faculty/miguel-hernan/causal-inference-book/

31. install.packages(“gdata”, dep = T)
library(gdata)
read.xls(“file.xls”)
Perl configuration necessary on Win
http://cran.r-project.org/web/packages/gdata/INSTALL

32. install.packages(“XLConnect”, dep = T)
library(XLConnect)
readWorksheet(loadWorkbook(“file.xls”),
sheet=1)
Define a function for simplicity
my.read.xls <- function(file) readWorksheet(loadWorkbook(file), sheet = 1)
my.read.xls(“file.xls”)
install.packages("XLConnect", type = "source") on Mac

33. To install a package
package name here
install.packages(“package”,
dep = T)
short for TRUE
short for dependencies

35. To load a package
package name here
library(package)
double quote “” can be omitted

36. Just click
box

37. Install package
Load package
Read xls file chosen to nhefs

39. install.packages(“sas7bdat”, dep = T)
library(sas7bdat)
read.sas7bdat(“file.sas7bdat”)
http://www.biostat.harvard.edu/~fitzmaur/ala2e/
smoking.sas7bdat

40. library(foreign)
read.xport(“file.xpt”)
ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/nhanes/
2009-2010/DEMO_F.xpt

42. library(foreign)
read.dta(“file.dta”)
http://www.biostat.harvard.edu/~fitzmaur/ala2e/
headache.dta

43. HTML table
http://
www.drugs.com/
top200_2003.html

44. install.packages(“XML”, dep = T)
library(XML)
readHTMLTable("http://www.drugs.com/top200_2003.html",
which = 2, skip.rows = 1)
http://www.drugs.com/top200_2003.html

45. Fixed width

46. read.fwf(“file.txt”,
width = c(3, 5, ...))
Use width = list(c(3,5,..), c(5,7,..))
for multiple rows per subject

47. Important functions
! install.packages(“PackageName”, dep = T)
! library(PackageName)
! str(dataset)
! summary(dataset)
! head(dataset)

49. Appendix:
Probability
Functions

50. what it
-norm -t -binom -pois does
density
d- dnorm dt dbinom dpois
(mass)
given x-
axis
return
p- pnorm pt pbinom ppois
probability,
given x-
axis(quan.)
return
q- qnorm qt qbinom qpois
quantile
(x-axis),
given prob.
library(BS t.test, return p-
-test DA):
z.test,
library(BS
DA):
binom.test poisson.test
value and
confidence
zsum.test tsum.test interval