how to use a scripting front-end for GNU R (original) (raw)

Examples

We show and discuss a few of the files in the examples/ directory of littler to. In a few cases we remove comment lines to keep things more concise on this page.

Simple Command-line Use

littler can be used directly on the command-line just like, say, bc:

echo 'cat(pi^2,"\n")' | r
9.869604

Equivalently, commands that are to be evaluated can be given on the command-line

r -e 'cat(pi^2, "\n")'
9.869604

But unlike bc(1), GNU R has a vast number of statistical functions. For example, we can quickly compute a summary() and show a stem-and-leaf plot for file sizes in a given directory via

ls -l /boot | awk 'BEGIN {print "size"} !/^total/ {print $5}' | \
     r -de "print(summary(X[,1])); stem(X[,1])"

which produces something like

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
     13     512  110100  486900  768400 4735000

  The decimal point is 6 digit(s) to the right of the |

   0 | 0000001122222279222
   2 | 79444
   4 | 71888
   6 |
   8 |
  10 |
  12 |
  14 | 8
  16 | 4
  18 |
  20 | 333

As we saw in the preceding example, the program can also be shortened like using the new -d option which reads from stdin and assigns to a data.frame named X.

And, last but not least, this (somewhat unwieldy) expression can be stored in a helper script (where we now switch to using an explicit readLines() on stdin):

#!/usr/bin/env r

fsizes <- as.integer(readLines(file("stdin")))
print(summary(fsizes))
stem(fsizes)

(where calling #!/usr/bin/env is a trick from Python which allows one to forget whether r is installed in /usr/bin/r, /usr/local/bin/r, ~/bin/r, …

CRAN package installation

Direct Installation

This is one of my favourite littler scripts which I use frequently to install packages off CRAN.

#!/usr/bin/env r

if (is.null(argv) | length(argv)<1) {
  cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n")
  q()
}

## adjust as necessary, see help('download.packages')
repos <- "http://cran.rstudio.com" 

## this makes sense on Debian where no packages touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"

install.packages(argv, lib.loc, repos)

I invoke it all the time with one, two or more packages to install (or reinstall).

$ install.r digest RcppCNPy

It conveniently installs all dependencies, and uses the chosen target directory, all while keeping my R prompt (or prompts with multiple sessions) free to do other things.

With Command-Line Parsing

Thanks to the fabulous docopt package, we also have a variant with optional settings of repo and location. Below is the updated version from littler 0.2.1:

#!/usr/bin/env r
#
# A second example to install one or more packages, now with option parsing
#
# Copyright (C) 2011 - 2014  Dirk Eddelbuettel
# Copyright (C) 2014         Carl Boettiger and Dirk Eddelbuettel
#
# Released under GPL (>= 2)

## load docopt package from CRAN
suppressMessages(library(docopt))       # we need docopt (>= 0.3) as on CRAN

## configuration for docopt
doc <- "Usage: install.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [--error] [PACKAGES ...]

-r --repos REPO     repository to install from [default: http://cran.rstudio.com]
-l --libloc LIBLOC  location in which to install [default: /usr/local/lib/R/site-library]
-d --deps DEPS      Install suggested dependencies as well [default: NA]
-e --error          Throw error and halt instead of a warning [default: FALSE]
-h --help           show this help text"

## docopt parsing
opt <- docopt(doc)

if (opt$deps == "TRUE" || opt$deps == "FALSE") {
    opt$deps <- as.logical(opt$deps)
} else if (opt$deps == "NA") {
    opt$deps <- NA
}

## installation given selected options and arguments

if (opt$error) {
    withCallingHandlers(
        install.packages(pkgs  = opt$PACKAGES,
                         lib   = opt$libloc,
                         repos = opt$repos,
                         dependencies=opt$deps),
        warning = stop)

} else { 
    install.packages(pkgs  = opt$PACKAGES,
                     lib   = opt$libloc,
                     repos = opt$repos,
                     dependencies=opt$deps)
}

Installing From Sources

Starting with version 0.2.2, install.r and install2.r now recognise installable source files. So one can also do this

$ install.r digest_0.6.8.tar.gz

and the local source file will the installed via a call to R CMD INSTALL.

Checking Packages

A related use case is to check packages via check.r. This script run R CMD check, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine.

GitHub package installation

Installation directly from GitHub is also popular, and now supported via a new helper script:

#!/usr/bin/env r
#
# A simple example to install one or more packages from GitHub
#
# Copyright (C) 2014         Carl Boettiger and Dirk Eddelbuettel
#
# Released under GPL (>= 2)

## load docopt and devtools from CRAN
suppressMessages(library(docopt))       # we need docopt (>= 0.3) as on CRAN
suppressMessages(library(devtools)) 

## configuration for docopt
doc <- "Usage: installGithub.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [PACKAGES ...]

-r --repos REPO     repository to install from [default: http://cran.rstudio.com]
-l --libloc LIBLOC  location in which to install [default: /usr/local/lib/R/site-library]
-d --deps DEPS      Install suggested dependencies as well? [default: NA]
-h --help           show this help text"

## docopt parsing
opt <- docopt(doc)
if(opt$deps == "TRUE" || opt$deps == "FALSE")
  opt$deps <- as.logical(opt$deps)
if(opt$deps == "NA")
  opt$deps <- NA

## installation given selected options and arguments
options(repos = opt$repos)
install_github(repo  = opt$PACKAGES,
               paste("-l =", opt$libloc),
               dependencies = opt$deps)

CRAN package update

One of the scripts I use the most (interactively) updates installed packages:

#!/usr/bin/env r 
#
# a simple example to update packages in /usr/local/lib/R/site-library
# parameters are easily adjustable

## adjust as necessary, see help('download.packages')
repos <- "http://cran.rstudio.com" 

## this makes sense on Debian where no package touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"

## r use requires non-interactive use
update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)

As above, it has my preferred mirror and library location hard-wired.

Calling knitr

Here is another convenience script which knits a given file after testing the file actually exists.

#!/usr/bin/r
#
# Simple helper script for knitr
#
# Dirk Eddelbuettel, May 2013
#
# GPL-2 or later

if (is.null(argv)) {
    cat("Need an argument FILE.Rnw\n")
    q(status=-1)
}


file <- argv[1]
if (!file.exists(file)) {
    cat("File not found: ", file, "\n")
    q(status=-1)
}

require(knitr)
knit2pdf(file)

Running roxygen

Similar to the previous example, this one uses roxygen to extract documentation from R files – either in the current directory, or in the given directory or directories.

#!/usr/bin/r
#
# Simple helper script for roxygen2::roxygenize() 
#
# Dirk Eddelbuettel, August 2013
#
# GPL-2 or later

## load roxygen
library(roxygen2)

## check all command-line arguments (if any are given) for directory status
argv <- Filter(function(x) file.info(x)$is.dir, argv)

## loop over all argument, with fallback of the current directory, and
## call compileAttributes() on the given directory
sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd")

Compiling Attributes

The next script can be used with Rcpp, and particularly is powerful Attributes feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes compileAttributes() instead.

#!/usr/bin/r
#
# Simple helper script for compileAttributes() 
#
# Dirk Eddelbuettel, July 2014
#
# GPL-2 or later

## load Rcpp
suppressMessages(library(Rcpp))

## check all command-line arguments (if any are given) for directory status
argv <- Filter(function(x) file.info(x)$is.dir, argv)

## loop over all argument, with fallback of the current directory, and
## call compileAttributes() on the given directory
sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes)

Initially created: Wed Aug 27 20:17:20 CDT 2014
Last modified: Sat May 30 08:26:28 CDT 2020