| Statistics::R(3pm) | User Contributed Perl Documentation | Statistics::R(3pm) |
Statistics::R - Perl interface with the R statistical program
Statistics::R is a module to controls the R interpreter (R project for statistical computing: <http://www.r-project.org/>). It lets you start R, pass commands to it and retrieve their output. A shared mode allows several instances of Statistics::R to talk to the same R process.
The current Statistics::R implementation uses pipes (stdin, stdout and stderr) to communicate with R. This implementation is more efficient and reliable than that in versions < 0.20, which relied on reading and writing intermediary files. As before, this module works on GNU/Linux, MS Windows and probably many more systems. Statistics::R has been tested with R version 2 and 3.
use Statistics::R;
# Create a communication bridge with R and start R
my $R = Statistics::R->new();
# Run simple R commands
my $output_file = "file.ps";
$R->run(qq`postscript("$output_file", horizontal=FALSE, width=500, height=500)`);
$R->run(q`plot(c(1, 5, 10), type = "l")`);
$R->run(q`dev.off()`);
# Pass and retrieve data (scalars or arrays)
my $input_value = 1;
$R->set('x', $input_value);
$R->run(q`y <- x^2`);
my $output_value = $R->get('y');
print "y = $output_value\n";
$R->stop();
use Statistics::R;
my $R1 = Statistics::R->new( shared => 1);
my $R2 = Statistics::R->new( shared => 1);
$R1->set( 'x', 'pear' );
my $x = $R2->get( 'x' );
print "x = $x\n";
$R1->stop; # or $R2->stop
Note that in shared mode, you are responsible for calling the stop() method from one of your Statistics::R instances when you are finished. But be careful not to call the stop() method if you still have processes that need to interact with R!
Example:
my $out = $R->run( q`print( 1 + 2 )` );
If you intend on running many R commands, it may be convenient to pass a list of commands or put multiple commands in an here-doc:
# List of R commands:
my $out1 = $R->run(
q`a <- 2`,
q`b <- 5`,
q`c <- a * b`,
q`print("ok")`
);
# Here-doc with multiple R commands:
my $cmds = <<EOF;
a <- 2
b <- 5
c <- a * b
print('ok')
EOF
my $out2 = $R->run($cmds);
Alternatively, to run commands from a file, use the run_from_file() method.
The return value you get from run() is a combination of what R would display on the standard output and the standard error, but the exact order may differ.
When loading modules, some may write numerous messages on standard error. You can disable this behavior using the following R command:
suppressPackageStartupMessages(library(library_to_load))
Note that older versions of R impose a limit on how many characters can be contained on a line: about 4076 bytes maximum. You will be warned if this occurs, with an error message stating:
'\0' is an unrecognized escape in character string starting "...
In this case, try to break down your R code into several smaller, more manageable statements. Alternatively, adding newline characters "\n" at strategic places in the R statements will work around the issue.
# Create an R scalar
$R->set( 'x', 'pear' );
or
# Create an R list
$R->set( 'y', [1, 2, 3] );
# Retrieve an R scalar. $x is a Perl scalar.
my $x = $R->get( 'x' );
or
# Retrieve an R list. $x is a Perl arrayref.
my $y = $R->get( 'y' );
Since Statistics::R relies on R to work, you need to install R first. See this page for downloads, <http://www.r-project.org/>. If R is in your PATH environment variable, then it should be available from a terminal and be detected automatically by Statistics::R. This means that you don't have to do anything on Linux systems to get Statistics::R working. On Windows systems, in addition to the folders described in PATH, the usual suspects will be checked for the presence of the R binary, e.g. C:\Program Files\R. If Statistics::R does not find where R is installed, your last recourse is to specify its full path when calling new():
my $R = Statistics::R->new( bin => $fullpath );
You also need to have the following CPAN Perl modules installed:
Florent Angly <florent.angly@gmail.com> (2011 rewrite)
Graciliano M. P. <gm@virtuasites.com.br> (original code)
Florent Angly <florent.angly@gmail.com>
Brian Cassidy <bricas@cpan.org>
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
All complex software has bugs lurking in it, and this program is no exception. If you find a bug, please report it on the CPAN Tracker of Statistics::R: <http://rt.cpan.org/Dist/Display.html?Name=Statistics-R>
Bug reports, suggestions and patches are welcome. The Statistics::R code is developed on Github (<http://github.com/bricas/statistics-r>) and is under Git revision control. To get the latest revision, run:
git clone git://github.com/bricas/statistics-r.git
| 2022-09-17 | perl v5.34.0 |