R FAQ

Kurt Hornik · official

     http://www.gnu.org/copyleft/gpl.html.
     
     http://www.ci.tuwien.ac.at/~hornik/R/
     
     rsync -rptC --delete rsync.R-project.org::module R
     
     $ ./configure
     $ make
     
     $ ./configure --prefix=/where/you/want/R/to/go
     
     deb http://cran.R-project.org/bin/linux/debian distribution main
     
     http://www.R-project.org/doc/bib/R.bib
     
     @Manual{,
       title        = {R: A language and environment for statistical
                       computing},
       author       = {{R Development Core Team}},
       organization = {R Foundation for Statistical Computing},
       address      = {Vienna, Austria},
       year         = 2004,
       note         = {ISBN 3-900051-00-3},
       url          = {http://www.R-project.org}
     }
     
     cube <- function(n) {
       sq <- function() n * n
       n * sq()
     }
     
     S> cube(2)
     Error in sq():  Object "n" not found
     Dumped
     S> n <- 3
     S> cube(2)
     [1] 18
     
     R> cube(2)
     [1] 8
     
     dorder <- function(n, r, pfun, dfun) {
       f <- function(x) NULL
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       PF <- call(substitute(pfun), as.name("x"))
       DF <- call(substitute(dfun), as.name("x"))
       f[[length(f)]] <-
         call("*", con,
              call("*", call("^", PF, r - 1),
                   call("*", call("^", call("-", 1, PF), n - r),
                        DF)))
       f
     }
     
     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       eval(substitute(function(x) K * PF(x)^a * (1 - PF(x))^b * DF(x),
                       list(PF = substitute(pfun), DF = substitute(dfun),
                            a = r - 1, b = n - r, K = con)))
     }
     
     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       function(x) {
         con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
       }
     }
     
     dorder <- function(n, r, pfun, dfun) {
       con <- round(exp(lgamma(n + 1) - lgamma(r) - lgamma(n - r + 1)))
       MC(function(x) {
            con * pfun(x)^(r - 1) * (1 - pfun(x))^(n - r) * dfun(x)
          },
          list(con = con, pfun = pfun, dfun = dfun, r = r, n = n))
     }
     
     MC <- function(f, env) f
     
     MC <- function(f, env = NULL) {
       env <- as.list(env)
       if (mode(f) != "function")
         stop(paste("not a function:", f))
       if (length(env) > 0 && any(names(env) == ""))
         stop(paste("not all arguments are named:", env))
       fargs <- if(length(f) > 1) f[1:(length(f) - 1)] else NULL
       fargs <- c(fargs, env)
       if (any(duplicated(names(fargs))))
         stop(paste("duplicated arguments:", paste(names(fargs)),
              collapse = ", "))
       fbody <- f[length(f)]
       cf <- c(fargs, fbody)
       mode(cf) <- "function"
       return(cf)
     }
     
          x <- 1; fun <- function() {y <- 1; ls()}
          
     $ R CMD INSTALL /path/to/pkg_version.tar.gz
     
     $ R CMD INSTALL -l lib /path/to/pkg_version.tar.gz
     
     R_LIBS="$HOME/lib/R:/usr/local/lib/R-contrib"; export R_LIBS
     
     R_LIBS="$HOME/lib/R:/usr/local/lib/R-contrib"
     
     library()
     
     Packages in `/home/me/lib/R':
     
     mystuff       My own R functions, nicely packaged but not documented
     
     Packages in `/usr/local/lib/R/library':
     
     KernSmooth    Functions for kernel smoothing for Wand & Jones (1995)
     MASS          Main Package of Venables and Ripley's MASS
     base          The R base package
     boot          Bootstrap R (S-Plus) Functions (Canty)
     class         Functions for Classification
     cluster       Functions for clustering (by Rousseeuw et al.)
     foreign       Read data stored by Minitab, S, SAS, SPSS, Stata, ...
     graphics      The R Graphics Package
     grid          The Grid Graphics Package
     lattice       Lattice Graphics
     methods       Formal Methods and Classes
     mgcv          Multiple smoothing parameter estimation and GAMs by GCV
     nlme          Linear and nonlinear mixed effects models
     nnet          Feed-forward Neural Networks and Multinomial Log-Linear
                   Models
     rpart         Recursive partitioning
     spatial       Functions for Kriging and Point Pattern Analysis
     splines       Regression Spline Functions and Classes
     stats         The R Stats Package
     stats4        Statistical functions using S4 classes
     survival      Survival analysis, including penalised likelihood
     tcltk         Tcl/Tk Interface
     tools         Tools for Package Development
     utils         The R Utils Package
     
     library(pkg)
     
     library(help = pkg)
     help(package = pkg)
     
     detach("package:pkg")
     
     $ R CMD REMOVE pkg_1 ... pkg_n
     
     $ R CMD REMOVE -l lib pkg_1 ... pkg_n
     
     set env R_HOME /opt/R
     set env R_PAPERSIZE letter
     set env R_PRINTCMD lpr
     dir /opt/R/src/appl
     dir /opt/R/src/main
     dir /opt/R/src/nmath
     dir /opt/R/src/unix
     
     x[i] <- list(NULL)
     
     rm(list = ls(all = TRUE))
     
     R> D(expression(x^2), "x")
     2 * x
     
     D2 <- function(e, n) D(D(e, n), n)
     
     g <- function(y) eval(substitute(y), sys.frame(sys.parent(n = 2)))
     g(a * b)
     
     rowmatrix <- mat[2, , drop = FALSE]  # creates a row matrix
     colmatrix <- mat[, 2, drop = FALSE]  # creates a column matrix
     a <- b[1, 1, 1, drop = FALSE]        # creates a 1 x 1 x 1 array
     
     somerows <- mat[index, ]
     
     somerows <- mat[index, , drop = FALSE]
     
     test1 <- function(x = pi, dig = 3) {
       oo <- options(digits = dig); on.exit(options(oo));
       cat(.Options$digits, x, "\n")
     }
     test2 <- function(x = pi, dig = 3) {
       .Options$digits <- dig
       cat(.Options$digits, x, "\n")
     }
     
     R> test1()
     3 3.14
     R> test2()
     3 3.141593
     
     as.numeric(as.character(f))
     
     as.numeric(levels(f))[as.integer(f)]
     
     title(substitute(hat(a) == ahat, list(ahat = ahat)))
     
     1+1
     
     summary(glm(y~x+z, family=binomial))
     
     print(1+1)
     
     print(summary(glm(y~x+z, family=binomial)))
     
     foo <- function(x, y, happy) {
       stopifnot(length(x) == 1, length(y) == 1) # scalars only!
       (x + y) * happy
     }
     
     wrapper <- function(x, y, my.fun, ...) {
       sapply(seq(along = x), FUN = function(i) my.fun(x[i], y[i], ...))
     }
     
     outer(1:4, 1:2, FUN = wrapper, my.fun = foo, happy = 10)
     
     varname <- c("a", "b", "d")
     
     get(varname[1]) + 2
     
     a + 2
     
     assign(varname[1], 2 + 2)
     
     a <- 2 + 2
     
     eval(substitute(lm(y ~ x + variable),
                     list(variable = as.name(varname[1]))
     
     lm(y ~ x + a)
     
     vars <- list(a = 1:10, b = rnorm(100), d = LETTERS)
     vars[["a"]]
     
     MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB *.c
     
     R> data.frame(x, y, z, monday, tuesday)

http://cran.at.R-project.org/	(TU Wien, Austria)
http://cran.au.R-project.org/	(PlanetMirror, Australia)
http://cran.br.R-project.org/	(Universidade Federal de Paraná, Brazil)
http://cran.ch.R-project.org/	(ETH Zürich, Switzerland)
http://cran.dk.R-project.org/	(SunSITE, Denmark)
http://cran.es.R-project.org/	(Spanish National Research Network, Madrid, Spain)
http://cran.fr.R-project.org/	(INRA, Toulouse, France)
http://cran.hu.R-project.org/	(Semmelweis U, Hungary)
http://cran.pt.R-project.org/	(Universidade do Porto, Portugal)
http://cran.uk.R-project.org/	(U of Bristol, United Kingdom)
http://cran.us.R-project.org/	(pair Networks, USA)
http://cran.za.R-project.org/	(Rhodes U, South Africa)

R FAQ

R FAQ

Frequently Asked Questions on R

Version 1.9-24 2004-06-15

ISBN 3-900051-01-1

1 Introduction

1.1 Legalese

1.2 Obtaining this document

1.3 Citing this document

1.4 Notation

1.5 Feedback

2 R Basics

2.1 What is R?

2.2 What machines does R run on?

2.3 What is the current version of R?

2.4 How can R be obtained?

2.5 How can R be installed?

2.5.1 How can R be installed (Unix)

2.5.2 How can R be installed (Windows)

2.5.3 How can R be installed (Macintosh)

2.6 Are there Unix binaries for R?

2.7 What documentation exists for R?

2.8 Citing R

2.9 What mailing lists exist for R?

2.10 What is CRAN?

2.11 Can I use R for commercial purposes?

2.12 Why is R named R?

2.13 What is the R Foundation?

3 R and S

3.1 What is S?

3.2 What is S-PLUS?

3.3 What are the differences between R and S?

3.3.1 Lexical scoping

3.3.2 Models

3.3.3 Others

3.4 Is there anything R can do that S-PLUS cannot?

3.5 What is R-plus?

4 R Web Interfaces

5 R Add-On Packages

5.1 Which add-on packages exist for R?

5.1.1 Add-on packages in R

5.1.2 Add-on packages from CRAN

5.1.3 Add-on packages from Omegahat

5.1.4 Add-on packages from Bioconductor

5.1.5 Other add-on packages

5.2 How can add-on packages be installed?

5.3 How can add-on packages be used?

5.4 How can add-on packages be removed?

5.5 How can I create an R package?

5.6 How can I contribute to R?

6 R and Emacs

6.1 Is there Emacs support for R?

6.2 Should I run R from within Emacs?

6.3 Debugging R from within Emacs

7 R Miscellanea

7.1 Why does R run out of memory?

7.2 Why does sourcing a correct file fail?

7.3 How can I set components of a list to NULL?

7.4 How can I save my workspace?

7.5 How can I clean up my workspace?

7.6 How can I get eval() and D() to work?

7.7 Why do my matrices lose dimensions?

7.8 How does autoloading work?

7.9 How should I set options?

7.10 How do file names work in Windows?

7.11 Why does plotting give a color allocation error?

7.12 How do I convert factors to numeric?

7.13 Are Trellis displays implemented in R?

7.14 What are the enclosing and parent environments?

7.15 How can I substitute into a plot label?

7.16 What are valid names?

7.17 Are GAMs implemented in R?

7.18 Why is the output not printed when I source() a file?

7.19 Why does outer() behave strangely with my function?

7.20 Why does the output from anova() depend on the order of factors in the model?

7.21 How do I produce PNG graphics in batch mode?

7.22 How can I get command line editing to work?

7.23 How can I turn a string into a variable?

7.24 Why do lattice/trellis graphics not work?

7.25 How can I sort the rows of a data frame?