R??

1
R????
?????? ???
2
R??

• ??????R??
• R???
• ?????
• ??
• ???????
• R?????
• R_GUI
• R_Commander
• R_WinEdt
• R_ESSXEmacs

3

• ??/??????
• John Verzani, Simple R Using R for Introductory
  Statistics, 2002 http//www.math.csi.cuny.edu/Sta
  tistics/R/simpleR/index.html
• J.H. Maindonald, Using R for Data Analysis and
  Graphics An Introduction, 2001
• Julian J. Faraway, Practical Regression and ANOVA
  Uing R, 2002http//www.stat.lsa.umich.edu/farawa
  y/????http//www.stat.lsa.umich.edu/faraway/
  stat500/introR.html
• S. Chatterjee, A.S. Hadi B. Price, Regression
  Analysis by Example, 3rd Ed., John Wiley Sons,
  2000http//www.ilr.cornell.edu/hadi/RABE/
• (???,???????,2003)

4
R??????
Robert Gentleman
Ross Ihaka
Bill Venables
5
??????R??

• R?
• ????(GPL)???????
• ????,?S??(?ATT Bell????Rick Becker, John
  Chambers,Allan Wilks??)?????(dialect)
  ??,????S-plus.
• ????,?????????????????????
• R??????(project),??(1995?)??Auckland??????Robert
  Gentleman?Ross Ihaka????,???R??????(R Development
  Core Team ???R DCT??)??,?????????????,??????????
  ?????????????????R?????(http//www.r-project.org)?
  ???R??????????,???????R?????R????????.

6

• R??????!! ?S-Plus??????????????,?????????US .
• R??????UNIX, Windows?Macintosh?????? .
• R??????????????.
• R?????????.
• ???R????????S-Plus???,??S??????????????R.
• ??R???????????,????????R?????.
• ?????????????????R??(??????????????!!)
• ....

7
??R???

• R?? http//www.r-project.org
• CRAN (Comprehensive R Archive Network),
• http//cran.r-project.org
• CRAN????? http//cran.r-project.org/mirrors.html
• UCLA?????R?S-Plus???,??????
• http//statcomp.ats.ucla.edu/splus/default.htm
  
• ????????R?Windows?? http//cn.math.pku.edu.cn/tea
  chers/lidf/index.html
• ????FTP??(?Cuteftp)?????(????)ftp.u-aizu.ac.jp

8
???????

• CRAN??????????????http//cran.r-project.org/src/
  contrib/PACKAGES.html
• stable -- ??(??)??????
• tseries ??????
• VaR ?????
• matrix ????
• cinterface C?R???
• foreign ???S, Minitab, SAS, SPSS, Stata??????
• normix ????????
• nortest ?????Anderson-Darling??
• MCMCpack ??Gibbs???MCMC????
• fracdiff ?????????????
• ????

9

• ????
• ?????pdf??(help-gtmanuals),?????
• W.N. Venables, D.M. Smith and the R DCT
  Introduction to R -- Notes on R A Programming
  Environment for Data Analysis and Graphics,
  2003.http//bayes.math.montana.edu/Rweb/Rnotes/R.
  html
• R DCT, The R Environment for Statistical
  Computing and Graphics -- Reference Index,2003.
• R DCT, R Data Import/Export, 2003.
• R DCT, R Language Definition,2003
• R DCT, Writing R Extensions,2003

10

• Kurt Hornik, R FAQ, Version 1.8-1, 2003-10-07
• B. D. Ripley, R for Windows FAQ, Version for
  rw1080
• R Html Help, Statistical Data Analysis
• ??PDF/HTML??
• Kickstarting R, http//cran.r-project.org/doc/cont
  rib/ Lemon-kickstart/
• R examples, Alison Gibbs, http//www.utstat.toron
  to.edu/alisong/Teaching/ Winter04/Sta248/Rex.html

11

• Ko-Kang Wang, Introduction to R for
  Statisticians,2004
• J.H. Maindonald, Using R for Data Analysis and
  Graphics An Introduction, 2001
• J.H. Maindonald, Using S-PLUS for Data Analysis
  and Graphics, 2001
• Emmanuel Paradis, R for beginners
• Jonathan Baron, R reference card
• Bret Larget, R for Introductory Statistics, 2002
• W. N. Venables and B. D. Ripley,Modern Applied
• Statistics with S,4th Ed., 2002
  http//www.stats.ox.ac.uk/pub/MASS4/

12

• ?????
• Peter Dalgaard, Introductory Statistics with R,
  Springer, 2002
• John Maindonald, John Braun, Data Analysis and
  Graphics Using R -- An Example-based Approach,
  Cambridge University Press,2003
• John Fox, An R and S-Plus Companion to Applied
  Regression, Sage Publications, Inc., 2002

13
R?????-1

• R_GUI
• ??R,????R GUI (graphic users interface)????,
  ???????
• ???
• ???
• R console (R?????)
• R console
• ????????????????????,????????,?????,???.
• ????????????
• help.start() HTML?????R?????
• help() ?????????,??help(plot)
• demo() ??R???????
• q() ??R
• ?Matlab??,??shift??????????

14

• ?????

Source R code
Load image
Save image
Copy and Paste
Stop current computation

• Source R code ??R??(.R?.r)
• Save image ??????,????.RData
• Load image ?????????
• Stop current computation ??????(???????)

15

• ?????

16
R?????-2

• R_Commander (????)
• ?? John Fox (jfox_at_mcmaster.ca)
• ??Rcmdr Version 0.9-0
• ??
• Rcmdr?R?????,??????car???
• ???Rcmdr????,???????car
• Rcmdr?????RGui (SDI)???,????RGui?EditgtGUI
  preferences????(??????)
• ??
• ????car
• ?RGui???PackagesgtLoad packages??Rcmdr??

17
(No Transcript)
18

• ??
• R Commander????????/?????(menu/dialog-box
  interfaces),?????????????????????.????????????????
  ??????.
• ?????(???Rcmdr?Getting Started??)
• R Commander????????????.
• ????????log/script??
• ??????????????RGUI?,??????????.???????log???????.?
  ??????????,????Rcmdr??????Submit????????R??
• ?????????????????.???????????,??????.???DatagtImp
  ort data?????,????????????,??R GUI?????!!

19

• R Commander???

R Commander ???(Menu Tree) (??)

• R Commander?????(information field)

20
R?????-3

• R_WinEdt ?????
• ?? Uwe Ligges (ligges_at_statistik.uni-dortmund.de)
  
• ??RWinEdt Version 1.6.0
• ????
• R http//cran.r-project.org/
• WinEdt5.x http//www.winedt.com/ (?CTeX2.3.x)
• R-WinEdt http//cran.r-project.org/contrib/extra/
  winedt/
• R_WinEdt???
• ?R_WinEdt???????WinEdt?plugins\R-WinEdt???
• ??install.exe????????,????WinEdt???????R.ini(?????
  winedt.exe!)
• ????????????CTeX2.3.x,???????,??WinEdt?
  C\CTeX\WinEdt ???

21

• R_WinEdt???
• ???????
• ????????LaTeX/CTeX?R_WinEdt,????????WinEdt???,
  ????R_WinEdt
• ??R_WinEdt???,????,?????(T)???
• C\CTeX\WinEdt\WinEdt -C"R-WinEdt" -er.ini
• (????)??????R??????/???????,???R????etc??.Rprofile
  ????,?????simple???????????
• library(simple)
• options(editor"\"c/program files/winedt/winedt\"
  
• -c\"R-WinEdt-edit\" -er.ini -V")

22
R_WinEdt ??
23
R_WinEdt ??
24

• R_WinEdt???
• - ?RGui????
• - ??WinEdt????? (?Delimiter??, ????, ??,?,
  ?????????)
• - ??????(Syntax-Highlighting)
• - ????????R??
• - ?????????????
• - ???????(script)???R???
• - WinEdt??????(code)???R???
• - ????(script)???R???
• - ???????????? .Rhistory,??????????
• - ??????,? for(_ in _)_

25

• R_WinEdt ?????
• Command Hot Key
  Menu Icon ??
• -------------------------------------------------
  --------------------------------------------------
  ---
• Brackets Check CtrlF12
  ??????
• R History ALTH
  R HIST. ??????
• R-line - and go ALTL
  ????
• R-line CtrlALTL
  ???????
• Rlt- R-paste - and go ALTP
  Rlt-PASTE ?????
• Rlt- R-paste CtrlALTP
  ????????
• Rlt- R-source - and go ALTS
  Rlt-SOURCE R????(???)
• Rlt- R-script CtrlALTS
  R SCRIPT R???????
• function CtrlAltF
  ??????
• for CtrlAltO
  ??for????
• if CtrlAltI
  ??if??
• ifelse CtrlAltE
  ??ifesle??
• lt- Ctrl-
  ??????

26
R?????-4

• R_ESSXEmacs ????? (?? John Fox)
• ??ESS?XEmacs
• Emacs???????????????,????????,??????,??(debugging)
  ?.
• For some Unix/Linux users, Emacs is more a
  way of life than an editor.
• ESS(Emacs Speaks Statistics)??????????????????,??R
  , S-Pplus, SAS, Stata, Lisp-Stat?.
• Emacs??????? GNU Emacs ? XEmacs.
• ?????ESS,??????????????????.
• John Fox?ESS??????????,???????
  ???????R????/??,?????????R??/???XEmacs???????????.
  (??????)
• XEmacs?ESS?????!

27
(No Transcript)
28

• ???????
• R http//cran.r-project.org/
• Xmacs with Ess http//www.xemacs.org/Download/win
  32/???Xemacs????(installer) setup.exe???,????net?
  ????Xemacs??????????????
• ess mail-lib
• dired pc
• ediff speedbar
• edit-utils vc
• efs xemacs-base
• fsf-compat xemacs-i586-pcwin32
• ??????????,?????????(local directory)

29

• XEmacs Netinstaller --- Install from the Internet
• Please note that these screenshots do not contain
  the latest version numbers for XEmacs, its
  packages and the installer itself. They are meant
  to give you a general idea of what the
  download/installation process will look like.
• An overview of existing packages and their
  purpose may be found at
• http//www.xemacs.org/Develop/packages.html
• and under the XEmacs source tree in etc/ PACKAGES.

????, ???New????????? ??????Skip???.
????????????????????.
????Native??(??Windows??Xemacs)
30

• R_ESSXEmacs???
• ????R?XEmacs??????
• R C\Program Files\R\rwxxxx\ (xxxx????)
• Xemacs C\Program Files\Xemacs
• ?????home??(WinXP/2000/NT???DOS?????? set HOME
  ??. ?????c\
• ?home????????(?DOS??mkdir) .xemacs
• ?John Fox?????????fox-ess-config.zip ,
• ???http//socserv.socsci.mcmaster.ca/jfox/Boo
  ks/Companion/ESS/index.html
• ?????init.el???Rinit.el???? .xemacs?

31

• ?????function.xpm, line.xpm, para.xpm,
  region.xpm, source.xpm?stop.xpm?????
• c\Program Files\Xemacs\XEmacs-xx.y.z\etc\
  toolbar\
• (xx.y.z?Xemacs????),???Xemacs???R????.
• (???)???????? c\Program Files\R\rwxxxx\bin
• (?WinXP/2000/NT???????gt??gt??gt???? ???/??).
• ???? ????????Rini.el????R???,? (setq-default
  inferior-R-program-name c/Program Files/
  rwxxxx/bin/rterm.exe) ----???????????().
• ??????XEmacs??? ???????????
• -q -l c\.xemacs\Rinit.el, ??????????????.

32

• ESSXEmacs?R??? ---??XEmacs??
• ???????
• ????R_XEmacs???????Initialization
  complete,????OK????.
• ??????????????(minibuffer?)?????????? .Rhistory
  ???. ????????????????R?ESS???(???????gt????????????
  ????!)

33
(No Transcript)
34

• ????
• John Fox?Xemacs???(?????frame)???????,????(?????).
  
• ?Xemacs?????????????(menu bar)??????(toolbar),????
  ????(buffer)???(major mode)???.???????????????????
  ????????.
• J. Fox?R????????????,??????(????).
• ????????scratch???,???????R??.????,
  scratch????????,???????????????.
• ????????R?Emacs?????,??????????????R??.

35

• ?????????????(mode line),????????,????1)?????
  2)??????(????) 3)?????????.
• ????????scratch buffer,??ESSS???(?????????????
  . S?S??,?????? ? .r, .R, .s, .S,
  .q?S??????,???ESSS????),????(ALL)?????????.
• ????????R buffer, ??iESS (inferior ESS
  ??????inferior,?????Emacs???!), ?????????(Bot).
  ???????????????.
• ??(point) Emacs???,?????????????,??John
  Fox?ESS????Windows????????.
• ???????????????,??minibuffer(???),????????,???????
  Emacs??,??????minibuffer?,?????(??????)???????.

36

• ESSXEmacs?R???
• --- R_XEmacs??
• Paste to R(???R)?? --- ????????????????????
• Paste line ???????
• Paste paragraph ????????(??????)
• Paste function ?????????????
• Paste region ??????????
• Source to R ???????(???)??????
• ??R??????????????????
• ??scratch buffer???????????
• (?????????)R?????????????????????????!
  ????????minibuffer???Process to load into
  R,??????
• Stop ??????(?????)

37

• R???
• ????/????R?????,????ESS??,??ESS???John
  Fox???R???R???.
• R????????????
• File ??
• Packages ??
• Misc ??
• ??????R GUI???

38

• ESSgtRgtFile??

• Source R code ???????????
• Save workspace ?R?????????
• Load workspace ?????????
• Change R directory ??????(?R??????,
  
  ??????????????)

39

• ESSgtRgtpackages??

• Load package ??R??,??????
• Install package from CRAN
  ?CRAN???.??.????(??internet??!)
• Install package from local zip file
  ???????????(zip????)
• Update packages from CRAN
  ?CRAN????? ????????????, ?????

40

• ESSgtRgtMisc??

• Remove all objects ??R??????????
• List objects
  ??R????????
• Display path ??R?????

• FilegtExit R/Xemacs??
• Quit saving R workspace ????R?????????
• Just quit
  ???R????????R,??? ???????????????

41
R????????

• ??
• ??
• gt ????????
• ???
• ??????
• ??
• - ??
• ??
• / ??
• ??
• ???
• ? lt-

42

• ???
• ?
• help()
• ??
• gt35
• gt3-5
• gt3/5
• gt35
• gtx5
• gt?plot
• gthelp(plot)

43

• ??
• ???R????????
• ??????????????,??
• ???
• ??
• ?????
• ?????
• ???
• ???
• ???

44

• ???????(??)
• seq() ? ???(??)?????????
• rep() ???(??)?????????
• c() ???(??)??????
• ??
• gt110
• gtseq(1,10,by0.5)
• gtseq(1,10,length21)
• gtrep(25,2)
• gtrep(25,rep(2,4))
• gtxc(42,7,64,9)
• gtlength(x)

45

• ??????????(recycling rule)
• gt1214
• gt1417

46

• ?????(index)?????(??)???
• ???? ??????????
• ???? ??????????
• ???? ????????????????
• ?R???????1??,????????????
• ????C?????????????????0??!
• ??
• gtx c(42,7,64,9)
• gtx1
• gtx-2
• gtxc(1,4)

47

• gtxgt10 ???10??????
• 1 TRUE FALSE TRUE FALSE
• gtxxgt10 ???10???
• 1 42 64
• gtxxlt40xgt10
• gt ??(0,1)?100????????
• gty runif(100, min 0, max 1)
• gtsum(ylt0.5) ???0.5??????
• 1 47
• gtsum(yylt0.5) ???0.5???????
• 1 10.84767

48

• ????(data frame)
• ???????????????
• ??????????????????????,?????,????????,???????
• ?????????(??)
• ???????????????,?????
• read.table() ?????????ASCII??
• ????????????,??????????
• read.csv() ?????????????(Comma
  Seperated values)
• read.delim() ????????tab????????
• ???????(?1,000,000??x200??),???
  ODBC????????.

49

• ???R???????????????????,?????data.frame(),?????cbi
  nd().
• ??
• gtxc(42,7,64,9)
• gty14
• gtz.dfdata.frame(cbind(INDEX y, VALUE x))
• gtz.df
• INDEX VALUE
• 1 1 42
• 2 2 7
• 3 3 64
• 4 4 9
• ? ? .df ????????z.df??????? ?
  INDEX?VALUE??????????

50

• ??????????
• ?? foorow, column?? foo ???????
  row ???????? column
  ????????
• ??(????)

gt z.df1, ???????(???)
INDEX VALUE 1 1 42 gt z.df,1
?????(???????) 1 1 2 3 4 gt z.df2,1
??????????? 1 2
51

• ??(list)
• ????????,????????????
• ???????????????
• R???(list)???????????
• ??
• gtfoo list(x 16, y matrix(14, nrow 2))
• gtfoo
• x
• 1 1 2 3 4 5 6
• y
• ,1 ,2
• 1, 1 3
• 2, 2 4

52

• ????????
• ????????foo?x,????????gt fooxgtfoo1gtfoo1
  ??
• gtfooy
• gtfoo2
• gtfoo2
• gtfoo12
• gtfooy2
• gtfooy4

53

• ????
• ?? ???????????????
• ??1 if (??) ???1 else ???2
• ??2 ?????1!ifelse(??, yes, no)
• ??????????gtx c(6-4)
• gt sqrt(ifelse(x gt 0, x, NA))
• gt ifelse(x gt 0, sqrt(x), NA)
• gtif (x gt 0) sqrt(x) else NA

54

• ??(loops)
• for() ???????for (?? in ??) ???
• while() ?????????while(??) ???
• ?????????1???????gtfor (i in 15) print
  (1i)gti1gtwhile(i lt 5) print(1i) i
  i1

55

• ?2 ?Ko-Kang Wangs R Programming Workshop,
  pp6-8
• Suppose we generate a pseudo DNA microarray and
  we want to do an ANOVA on it. First we generate
  some factors for Array (a), Treatments (t) and
  Genes (g). Then generate some normal random
  numbers for the logged foreground intensity. Then
  we put into an aov() function for each gene
  this is where the loop is good for. Note that you
  will get different answer when you try it,
  because of the random numbers generated.
• ????(??for??,????while??)DNA_anova.R?R????????
  ?gt?,??????????!

56

• gt n 3044
• gt a c(rep(1, 2 n), rep(2, 2 n))
• gt t c(rep(1, n), rep(2, n), rep(2, n), rep(1,
  n))
• gt g rep(rep(11522, rep(2, 1522)), 4)
• gt y rnorm(4 n, mean 4.13, sd 0.75)
• gt ybar data.frame(A factor(a), G
  factor(g),
• T factor(t), Intensity y)
• gt attach(ybar)
• gt ybar110, ??ybar??10?
• gt res.mat matrix(0, 1522, 8, byrow TRUE)
• gt coef.mat matrix(0, 1522, 4, byrow TRUE)
• gt for(i in 11522)
• gene.aov aov(Intensity A T A T,
• sub G i)
• res.mati, residuals(gene.aov)
  ??ANOVA?????
• coef.mati, coef(gene.aov)
  ??ANOVA???????
• gt res.mat110, ??????10?
• gt coef.mat110, ????????10?

57

• ???(vectorization)
• ??(loops)???,????????????,????????,????
• C???????,???????R?????????????,??C??R?100??
• ?R????????,??R?????C????,???????????!
• ?? --?Ko-Kang Wangs R Programming Workshop,
  pp9-11 (Gamma????)
• Vector_1.R ?????????????
• Vector_2.R ??for?????????
• Vector_3.R ?????????

58

• ??
• ???????????,?R??????????
• ?? ??? function( ???? ) ???
• ???? ???(????)
• ????????,????!
• ?? ??gamma???n!gtfactorial function(n)
• if (ngt0) gamma(n1)
• else print(Please input a positive
  integer!")
• gtfactorial(6)
• gtfactorial(-6)

59

• ????????? ??????????????????????
• warning() ??????????????
• stop() ???????????
• print() ???????
• formatC() ?????????
• cat() ????,????\n(??)?\t(tab?)
• paste() ????(????????)??gtcat("R",
  "is","a good", "software.\n")
• gtformatC(1/3, format "f", digits 4)gt
  formatC(1/3, format "e", digits
  4)gtpaste(112) ?as.character(112)??gtpaste("A
  ", 16, sep "")gtpaste("today is", date())

60
R????

• ??????
• ??????(?)???????????????,???????????
• ?????????!!
• ??!!
• ??!!
• SAS???????????????????,?!!??SAS??????,?SPSS??!
• ????????(??)????????????

61

• ??????
• ????,?????! ????????
• ???(readability)
• ????(understandability)
• ????????(Indentation),????????
• WinEdt gt ??????WinEdt?R????
• (X)Emacs gt??????(X)Emacs?R????
• UltraEdit
• ????????(Commenting),??????
• R????????????.
• ?????????,?????????,???????????

62

• ?? ??
• gt for(i in 11522)
• gene.aov lt- aov(Intensity A T A T,
• sub G i)
• res.mati, lt- residuals(gene.aov)
• coef.mati, lt- coef(gene.aov)
• ?
• gtfor(i in 11522)
• gt
• gene.aov lt- aov(Intensity A T A T,
• sub G i)
• res.mati, lt- residuals(gene.aov)
• coef.mati, lt- coef(gene.aov)

63

• ????
• 1.Julian Faraway??????????
• Introduction to R
• ?? R GUI
• ?? R Commander
• ?? R_XEmacs
• Further reference Moore's The Basic Practice of
  Statistics, Second
  Edition (Freeman, 2000),
• 2. John Verzani ???????? SimpleR --- Using R
  for Introductory Statistics
• ??R_WinEdt