NAME

R::YapRI.pm Just the doc. for R::YapRI modules.

SYNOPSIS

 use R::YapRI::Base;

 ## WORKING WITH THE DEFAULT MODE:

 my $rbase = R::YapRI::Base->new();
 $rbase->add_command('bmp(filename="myfile.bmp", width=600, height=800)');
 $rbase->add_command('dev.list()');
 $rbase->add_command('plot(c(1, 5, 10), type = "l")');
 $rbase->add_command('dev.off()');

 $rbase->run_command();
 
 my $result_file = $rbase->get_result_file();
 
 ## To work with blocks, check R::YapRI::Block

DESCRIPTION

Yet another perl wrapper to interact with R. R::YapRI are a collection of modules to interact with R using Perl.

The mechanism is simple, it write R commands into a command file and executate it using the R as command line: R [options] < infile > outfile

use R::YapRI::Base;
my $rbase = R::YapRI::Base->new();
$rbase->add_command('x <- c(1:10)');
$rbase->add_command('y <- c(2,3,5,7,11,13,17,19,23,29)');
$rbase->add_command('x * y');
my $resultfile = $rbase->get_result_file();

But there are some tricks, it can define blocks and combine them, so it can extend the interaction between packages of information. For example, it can create a block to check the length of a vector using default as base

my $newblock = $rbase->create_block('lengthblock', 'default');
$newblock->add_command('length(x * y)');
$newblock->run_block();
my @results = $newblock->read_results();

if ($results[0] == 10) {
   my $newblock2 = $rbase->create_block('meanblock', 'default');
   $newblock2->add_command('z <- mean(x * y)');
   $newblock2->run_block();
   my @results2 = $newblock2->read_results();
}

It can use interpreters (R::YapRI::Interpreter::Perl), so sometimes it can use perl hashref. instead strings to add_commands.

$rbase->add_command('mean(c(2,3,5,7,11,13,17,19,23,29))');
$rbase->add_command({ mean => [2,3,5,7,11,13,17,19,23,29]});

It uses two switches to trace the R commands that you are running: - disable_keepfiles/enable_keepfiles, to do not delete the command files and the result files after the executation of the code. - disable_debug/enable_debug, to print as STDERR the R commands from the command file before executate them.

AUTHOR

Aureliano Bombarely <ab782@cornell.edu>

COPYRIGHT AND LICENCE

Copyright 2009 Boyce Thompson Institute for Plant Research

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.