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Installing R

Installing R. CRAN: http://cran.r-project.org/ (R homepage: http://www.r-project.org/ ) Windows 95 and later  Base rw2001.exe. Editors for R. WinEdt www.winedt.com Download winedt 5.3 or 5.4 RWinEdt package http://cran.r-project.org/  Other  Editing Support  R-WinEdt

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Installing R

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  1. Installing R • CRAN: http://cran.r-project.org/ • (R homepage: http://www.r-project.org/) • Windows 95 and later  Base • rw2001.exe

  2. Editors for R • WinEdt • www.winedt.com • Download winedt 5.3 or 5.4 • RWinEdt package • http://cran.r-project.org/ Other  Editing Support  R-WinEdt • Download most recent zip file • Packages  Install package(s) from local zip files • Library(RWinEdt) • To make automatic: R rw2001  etc  Rprofile • Type commands, highlight, R-Paste • Use ## for comments • Free for about 100 uses, student license is $30 • EMACS • www.xemacs.org • ESS package • Free!

  3. General • R workspace • Show what’s been stored: ls() or objects() • Remove individual objects: rm(a, b, etc.) • Clear entire workspace: rm(list=ls()) • Quit: q() or file  exit • Save workspace? • Where to store R files: file  change directory • File  load workspace or save workspace • save() or save.image() • Up arrow repeats prior commands • R is case sensitive • “>” – start new command; “+” – finish command • Customize R • Options() • Edit  GUI preferences

  4. Assignments and some basic math • The assignment operator consists of ‘<‘ and ‘-’ and points from the expression to the name given to that expression • x <- 10 assigns the number 10 to the letter x • Assignments can be made in either direction • R as an over-qualified calculator • Log, exp • Mean, median, mode, max, min, sd • Trigonometry • Set operations • Logical operators: <, <=, >, >=, ==, !=

  5. Vectors • Vectors have length, but no dimension • >length(vector) • c() concatenates or combines numbers inside () into a vector or list • seq() generates sequence • Can specify length of sequence and increment • rep() replicates elements • >sort(vector) sorts items in vector • Can use usual arithmetic and mathematical functions on vectors • Logical vectors • Character vectors • Indexing a vector: • >vector[i]

  6. Matrices • Matrices have length and dimensions • >length(M); dim(M) • Generating matrices • By combining vectors: rbind(); cbind() • >matrix() command • Transpose • >t(M) • Diagonal • >diag(M) • Inverse • >solve(M) • Multiplying matrices: M%*%N • Indexing matrices

  7. Some simple functions • Writing a user function • >function( argument list ){expressions} • Expressions or commands can be grouped together in {}, as they often are when writing functions. The value of the grouped commands is the result of the last expression. • Conditionals • ‘if’, ‘else’ • Loops • ‘for’

  8. Probability distributions • norm, binom, beta, cauchy, chisq, exp, f, gamma, geom, hyper, lnorm, logis, nbinom, t, unif, weibull, wilcox • Four prefixes: • ‘d’ for density (PDF) • ‘p’ for distribution (CDF) • ‘q’ for quantile (percentiles) • ‘r’ for random generation (simulation) • Each distribution has arguments that need to be specified

  9. Loading • Stata, SPSS, SAS files • Library(foreign) • Stata: read.dta • SPSS: read.spss • SAS: read.xport (must first create export file in SAS) • Excel files • Files must be saved as comma separated value or .csv • read.table, read.csv, read.csv2: identical except for defaults • Watch the direction of ‘/’! • >load(“.Rdata”) • Loading and running R programs • >source(“.R”)

  10. Data • >summary(data) • >names(data); >attributes(data) • Editing data • >fix(data) or >edit(data) • >data$var • >attach(data) in order to remove need of ‘$’ • >detach(data)

  11. NA, NaN, and Null • NA or “Not Available” • Applies to many modes – character, numeric, etc. • NaN or “Not a Number” • Applies only to numeric modes • NULL • Lists with zero length

  12. Lm, glm, nlm, optim • Linear models • >lm(y~x1+x2) • Generalized linear models • >glm(y~x1+x2, family=“”) • See help(family) for family options; family specifies error distribution • Non-linear minimization • >nlm(f, p) where f is the function to be minimized and p are the starting parameters • Optimization • >optim(par, fn) where par are the initial values and fn is the function to be minimized

  13. Graphics • >par() is used to set graphical options • mfrow and mfcol • >plot(x,y) • >identify(); >abline() • Arguments: type, point style, labels, etc. • Boxplot, histograms, sunflowerplots, piecharts, etc. • Saving them • As .pdf or .ps files • >dev.off() • Know the current directory

  14. Help! • >help(package=stats) • Lists functions in the specified package • >help(glm) or >?glm • >help(“{“) for characters • Help  Html help  Search Engine & Keywords • Potentially most helpful • R documentation • command{package}

  15. Other Resources • The R Manuals under Documentation at http://www.r-project.org • Mark Handcock’s website at http://www.stat.washington.edu/handcock/567/links.html • Jonathan Barron’s R resources at http://finzi.psych.upenn.edu/ • Fox, John. 2002. An R and S-PLUS Companion to Applied Regression • Cori Mar is teaching an intro to R class in the main CSSCR lab on Wednesday from 3:30-5

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