R FAQ ¶

p

https://www.R-project.org/Licenses/

https://CRAN.R-project.org/doc/manuals/

@Misc{,
  author        = {Kurt Hornik and the R Core Team},
  title         = {{R} {FAQ}},
  year          = {2024},
  url           = {https://CRAN.R-project.org/doc/manuals/R-FAQ.html}
}

John Chambers,
Peter Dalgaard,
Robert Gentleman,
Kurt Hornik,
Ross Ihaka,
Tomas Kalibera,
Michael Lawrence,
Uwe Ligges,
Thomas Lumley,
Martin Maechler,
Sebastian Meyer,
Paul Murrell,
Martyn Plummer,
Brian Ripley,
Deepayan Sarkar,
Duncan Temple Lang,
Luke Tierney, and 
Simon Urbanek,

$ ./configure
$ make

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

https://www.R-project.org/doc/bib/R.bib

@Manual{,
  title        = {R: A Language and Environment for Statistical
                  Computing},
  author       = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address      = {Vienna, Austria},
  year         = YEAR,
  url          = {https://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          Support Functions and Datasets for 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)
boot          Bootstrap Functions (Originally by Angelo Canty for S)
class         Functions for Classification
cluster       "Finding Groups in Data": Cluster Analysis Extended
              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", unload = TRUE)

$ 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.names = 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
R> print(a * a, digits = 18)
[1] 2.00000000000000044

R> .3 + .6 == .9
[1] FALSE
R> .3 + .6 - .9
[1] -1.110223e-16
R> print(matrix(c(.3,  .6,  .9, .3 + .6)), digits = 18)
                     [,1]
[1,] 0.299999999999999989
[2,] 0.599999999999999978
[3,] 0.900000000000000022
[4,] 0.899999999999999911

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 GraphicsAntialias 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

local({r <- getOption("repos")
       r["CRAN"] <- "http://CRAN-archive.R-project.org"
       options(repos = r)
      })

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

R FAQ ¶

Table of Contents

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-like) ¶

2.5.2 How can R be installed (Windows) ¶

2.5.3 How can R be installed (Mac) ¶

2.6 Are there Unix-like 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 Bioconductor ¶

5.1.4 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? ¶

7.25 Why did my .Rprofile stop working when I updated R? ¶

7.26 Where have all the methods gone? ¶

7.27 How can I create rotated axis labels? ¶

7.28 Why is read.table() so inefficient? ¶

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

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

7.35 Why are p-values not displayed when using `lmer()`? ¶