R Programming/Utilities

This page includes material about some utilities. Most of the functions presented here have nothing to do with statistical analysis but may be useful when working on a project. Many functions are just similar to standard unix functions.

System (Unix/DOS)

system() gives access to the system (DOS or unix). The option wait=FALSE means that you don't ask R to wait that the task is finished.

Some examples :

• You can convert an image from to PS to PNG using the unix convert function of your computer. If you want to know more about this function, open a Terminal application and type man convert (This should work on Mac OS and Linux).
• You can open Stata and run a program.
• You can run pdflatex from R and directly open the pdf in a pdf browser.

system("convert W:/toto.ps W:/toto.png") # converts toto.ps to toto.png
system("D:/Stata10/stata.exe do D:/pgm.do", wait = F) # opens Stata and run pgm.do
system("pdflatex.exe -shell-escape file.tex") # runs pdflatex
system("open file.pdf") # opens the pdf
system("open M:/.../doc/*.pdf") # opens all the pdf in a directory

See also sys() in the Hmisc package, shell() and shell.exec().

File Handling

dir() lists all the files in a directory. It is similar to the Unix function ls. dir.create() creates a new directory. It is similar to mkdir in Unix.

file.info() gives information about a file.

> file.info("taille.txt")
           size isdir mode               mtime               ctime               atime exe
taille.txt  444 FALSE  666 2009-06-26 12:25:44 2009-06-26 12:25:43 2009-06-26 12:25:43  no

Removing files with a specific pattern :

file.remove(dir(path="directoryname", pattern="*.log"))

• file.edit() opens a file in the text editor.
• file.show() opens a file in a new window.
• tempfile() creates a temporary file.

• getZip() in the Hmisc package.

Internet

browseURL() opens an URL using an internet browser. download.file() download a file from the internet.

> browseURL("http://en.wikibooks.org/wiki/R_Programming")

To see the default browser, use getOption()

getOption("browser")

We can change the default browser using the options() command. It is safer to store the options before.

oldoptions <- options() # save the options
options(browser = "D:/FramafoxPortable/FramafoxPortable.exe")

You can download a file from the internet using download.file(). Note that very often you don't need to download a file from the internet and you can directly load it into R from the internet using standard functions. For instance, if you want to read a text file from the internet, you can use read.table(), scan() or readLines().

# For example, we download "http://en.wikibooks.org/wiki/R_Programming/Text_Processing" on our Desktop
download.file(url="http://www.http://en.wikibooks.org/wiki/R_Programming/Text_Processing",destfile= "~/Desktop/test_processing.html")
# You can also read it into R using readLines()
text <- readLines("http://www.http://en.wikibooks.org/wiki/R_Programming/Text_Processing")

See also RCurl

Computing time

If you perform computer intensive task you may want to optimize the computing time. Two functions are available system.time() and proc.time(). Both returns a vector of values. The first is the standard CPU time.

> system.time(x<-rnorm(10^6))
[1] 1.14 0.07 1.83 0.00 0.00

> debut <- proc.time()
> x <- rnorm(10^6)
> proc.time()-debut
[1]  1.66  0.10 10.32  0.00  0.00

Computing process

user.prompt() (Zelig) makes a pause in the computation process (useful if you want to do a demo). waitReturn() (cwhmisc) does the same job. Sys.sleep() stop the computation during a few seconds.

> user.prompt()
 
Press <return> to continue: 
> Sys.sleep(5)

It is possible to stop the computing process if a logical condition is not true using stopifnot().

Miscellanous

• trCopy() (TinnR package) copy an object to the clipboard. It is useful if you want to copy a large object to the clipboard. For instance, if you want to copy the code of a function and paste it in a text editor.

> trCopy(lm)
[1] TRUE

• sessionInfo() gives information on the current session info (R version + loaded packages). This function may be useful for reproducible computing. getRversion() gives the current R version. R.version gives more details about the computer and R.Version() returns the same informations as a list.

See Also

• See the R.utils package