R FAQ

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

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

@Misc{,
  author        = {Kurt Hornik},
  title         = {{R} {FAQ}},
  year          = {2020},
  url           = {https://CRAN.R-project.org/doc/FAQ/R-FAQ.html}
}

$ ./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          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", 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 = 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

options(download.file.method = "wininet", url.method = "wininet")
(Windows)
options(download.file.method = "libcurl", url.method = "libcurl")
(Linux and macOS)

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

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

• Introduction:
• R Basics:
• R and S:
• R Web Interfaces:
• R Add-On Packages:
• R and Emacs:
• R Miscellanea:
• R Programming:
• R Bugs:
• Acknowledgments:

• Legalese:
• Obtaining this document:
• Citing this document:
• Notation:
• Feedback:

• What is R?:
• What machines does R run on?:
• What is the current version of R?:
• How can R be obtained?:
• How can R be installed?:
• Are there Unix-like binaries for R?:
• What documentation exists for R?:
• Citing R:
• What mailing lists exist for R?:
• What is CRAN?:
• Can I use R for commercial purposes?:
• Why is R named R?:
• What is the R Foundation?:
• What is R-Forge?:

	CPU	Versions	Provider
Debian	i386/amd64	squeeze/wheezy	Johannes Ranke
	armel	wheezy	Johannes Ranke
Ubuntu	i386/amd64	lucid/precise/trusty	Michael Rutter

• What is S?:
• What is S-PLUS?:
• What are the differences between R and S?:
• Is there anything R can do that S-PLUS cannot?:
• What is R-plus?:

• How can R be installed (Unix-like):
• How can R be installed (Windows):
• How can R be installed (Mac):

• Which add-on packages exist for R?:
• How can add-on packages be installed?:
• How can add-on packages be used?:
• How can add-on packages be removed?:
• How can I create an R package?:
• How can I contribute to R?:

• Add-on packages in R:
• Add-on packages from CRAN:
• Add-on packages from Bioconductor:
• Other add-on packages:

• Is there Emacs support for R?:
• Should I run R from within Emacs?:
• Debugging R from within Emacs:

• How can I set components of a list to NULL?:
• How can I save my workspace?:
• How can I clean up my workspace?:
• How can I get eval() and D() to work?:
• Why do my matrices lose dimensions?:
• How does autoloading work?:
• How should I set options?:
• How do file names work in Windows?:
• Why does plotting give a color allocation error?:
• How do I convert factors to numeric?:
• Are Trellis displays implemented in R?:
• What are the enclosing and parent environments?:
• How can I substitute into a plot label?:
• What are valid names?:
• Are GAMs implemented in R?:
• Why is the output not printed when I source() a file?:
• Why does outer() behave strangely with my function?:
• Why does the output from anova() depend on the order of factors in the model?:
• How do I produce PNG graphics in batch mode?:
• How can I get command line editing to work?:
• How can I turn a string into a variable?:
• Why do lattice/trellis graphics not work?:
• How can I sort the rows of a data frame?:
• Why does the help.start() search engine not work?:
• Why did my .Rprofile stop working when I updated R?:
• Where have all the methods gone?:
• How can I create rotated axis labels?:
• Why is read.table() so inefficient?:
• What is the difference between package and library?:
• I installed a package but the functions are not there:
• Why doesn't R think these numbers are equal?:
• How can I capture or ignore errors in a long simulation?:
• Why are powers of negative numbers wrong?:
• How can I save the result of each iteration in a loop into a separate file?:
• Why are p-values not displayed when using lmer()?:
• Why are there unwanted borders:
• Why does backslash behave strangely inside strings?:
• How can I put error bars or confidence bands on my plot?:
• How do I create a plot with two y-axes?:
• How do I access the source code for a function?:
• Why does summary() report strange results for the R^2 estimate when I fit a linear model with no intercept?:
• Why is R apparently not releasing memory?:
• How can I enable secure https downloads in R?:
• How can I get CRAN package binaries for outdated versions of R?:

• How should I write summary methods?:
• How can I debug dynamically loaded code?:
• How can I inspect R objects when debugging?:
• How can I change compilation flags?:
• How can I debug S4 methods?:

• Lexical scoping:
• Models:
• Others:

R FAQ

Frequently Asked Questions on R

Version 2020-08-03

Kurt Hornik

Table of Contents

R FAQ

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?