/ 
R-YapRI-0.04
River stage zero No dependents
/ R::YapRI

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>

ACKNOWLEDGEMENTS

Lukas Mueller Robert Buels Naama Menda Jonathan "Duke" Leto

COPYRIGHT AND LICENCE

Copyright 2011 Boyce Thompson Institute for Plant Research Copyright 2011 Sol Genomics Network (solgenomics.net)

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