R FAQ

Kurt Hornik · official

     http://www.gnu.org/copyleft/gpl.html.

     http://CRAN.R-project.org/doc/FAQ/

     @Misc{,
       author        = {Kurt Hornik},
       title         = {The {R} {FAQ}},
       year          = {2009},
       note          = {{ISBN} 3-900051-08-9},
       url           = {http://CRAN.R-project.org/doc/FAQ/R-FAQ.html}
     }

     $ ./configure
     $ make

     $ ./configure --prefix=/where/you/want/R/to/go

     Protocol: HTTP
     Server name: software.openSUSE.org
     Directory: /download/home:/dsteuer/openSUSE_10.2/

     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         = 2009,
       note         = {{ISBN} 3-900051-07-0},
       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/pkg_version.tar.gz

     $ R CMD INSTALL -l lib path/pkg_version.tar.gz

     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
          Matrix        Sparse and Dense Matrix Classes and Methods
          base          The R Base package
          boot          Bootstrap R (S-Plus) Functions (Canty)
          class         Functions for Classification
          cluster       Functions for clustering (by Rousseeuw et al.)
          codetools     Code Analysis Tools for R
          datasets      The R Datasets Package
          foreign       Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat,
                        dBase, ...
          grDevices     The R Graphics Devices and Support for Colours and Fonts
          graphics      The R Graphics Package
          grid          The Grid Graphics Package
          lattice       Lattice Graphics
          methods       Formal Methods and Classes
          mgcv          GAMs with GCV/AIC/REML smoothness estimation and GAMMs
                        by PQL
          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)))

     title(bquote(hat(a) = .(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"]]

     ps.options(horizontal = FALSE)
     help.start()

     grDevices::ps.options(horizontal = FALSE)
     utils::help.start()

     getS3method("[", "terms")

     ## Increase bottom margin to make room for rotated labels
     par(mar = c(7, 4, 4, 2) + 0.1)
     ## Create plot with no x axis and no x axis label
     plot(1 : 8, xaxt = "n",  xlab = "")
     ## Set up x axis with tick marks alone
     axis(1, labels = FALSE)
     ## Create some text labels
     labels <- paste("Label", 1:8, sep = " ")
     ## Plot x axis labels at default tick marks
     text(1:8, par("usr")[3] - 0.25, srt = 45, adj = 1,
          labels = labels, xpd = TRUE)
     ## Plot x axis label at line 6 (of 7)
     mtext(1, text = "X Axis Label", line = 6)

     R> a <- sqrt(2)
     R> a * a == 2
     [1] FALSE
     R> a * a - 2
     [1] 4.440892e-16

     beta[i,] <- tryCatch(coef(lm(formula, data)),
                          error = function(e) rep(NaN, 4))

     R> -2^2
     [1] -4

     R> (-2)^2
     [1] 4

     R> as.list(quote(-2^2))
     [[1]]
     `-`
     
     [[2]]
     2^2

     for(i in 1:100) {
       ## Calculations constructing "some_object" ...
       fp <- file.path("Results", paste("result", i, ".rda", sep = ""))
       save(list = "some_object", file = fp)
     }

          $ kwriteconfig --file okularpartrc --group 'Dlg Performance' \
                         --key TextAntialias Disabled
     
     > str <- "This \"text\" is quoted"
     > str
     [1] "This \"text\" is quoted"
     > cat(str, "\n")
     This "text" is quoted

     > nchar("\n")
     [1] 1
     > substring("\n", 1, 1)
     [1] "\n"

     > cat("\\n", "\n")
     \n

     R> data.frame(x, y, z, monday, tuesday)

	CPU	Versions	Provider
Debian	i386/amd64	etch-cran	Johannes Ranke
	i386	lenny-cran	Johannes Ranke
Red Hat	i386/x86_64	fedora8/fedora9/fedora10	Martyn Plummer
	i386/x86_64	el4/el5	Bob Kinney
SuSE	i586/x86_64	10.3/11.0/11.1	Detlef Steuer
Ubuntu	i386	dapper/gutsy/hardy/intrepid	Vincent Goulet
	amd64	dapper/gutsy/hardy/intrepid	Michael Rutter

http://cran.at.R-project.org/	(WU Wien, Austria)
http://cran.au.R-project.org/	(PlanetMirror, Australia)
http://cran.br.R-project.org/	(Universidade Federal do 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.pt.R-project.org/	(Universidade do Porto, Portugal)
http://cran.uk.R-project.org/	(U of Bristol, United Kingdom)
http://cran.za.R-project.org/	(Rhodes U, South Africa)

R FAQ

R FAQ

Frequently Asked Questions on R

Version 2.10.2009-12-10

ISBN 3-900051-08-9

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?

2.14 What is R-Forge?

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 How can I set components of a list to NULL?

7.2 How can I save my workspace?

7.3 How can I clean up my workspace?

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

7.5 Why do my matrices lose dimensions?

7.6 How does autoloading work?

7.7 How should I set options?

7.8 How do file names work in Windows?

7.9 Why does plotting give a color allocation error?

7.10 How do I convert factors to numeric?

7.11 Are Trellis displays implemented in R?

7.12 What are the enclosing and parent environments?

7.13 How can I substitute into a plot label?

7.14 What are valid names?

7.15 Are GAMs implemented in R?

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

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

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

7.19 How do I produce PNG graphics in batch mode?

7.20 How can I get command line editing to work?

7.21 How can I turn a string into a variable?

7.22 Why do lattice/trellis graphics not work?

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

7.24 Why does the help.start() search engine not work?