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MANIFEST
META.yml
MYMETA.json
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Makefile.PL
README

README

NAME
    Statistics::R - Perl interface with the R statistical program

DESCRIPTION
    *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.

SYNOPSIS
      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();

METHODS
    new()
        Build a *Statistics::R* bridge object connecting Perl and R.
        Available options are:

        bin Specify the full path to the R executable, if it is not
            automatically found. See "INSTALLATION".

        shared
            Start a shared bridge. When using a shared bridge, several
            instances of Statistics::R can communicate with the same unique
            R instance. Example:

               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!

    run()
        First, *start()* R if it is not yet running. Then, execute R
        commands passed as a string and return the output as a string. If
        your commands failed to run in R, an error message will be
        displayed.

        Example:

           my $out = $R->run( q`print( 1 + 2 )` );

        If you intend on runnning 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.

    run_from_file()
        Similar to *run()* but reads the R commands from the specified file.
        Internally, this method converts the filename to a format compatible
        with R and then passes it to the R *source()* command to read the
        file and execute the commands.

    result()
        Get the results from the last R command.

    set()
        Set the value of an R variable (scalar or vector). Example:

          # Create an R scalar
          $R->set( 'x', 'pear' );

        or

          # Create an R list
          $R->set( 'y', [1, 2, 3] );

    get()
        Get the value of an R variable (scalar or vector). Example:

          # 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' );

    start()
        Explicitly start R. Most times, you do not need to do that because
        the first execution of *run()* or *set()* will automatically call
        *start()*.

    stop()
        Stop a running instance of R. You need to call this method after
        running a shared bridge. For a simple bridge, you do not need to do
        this because *stop()* is automatically called when the Statistics::R
        object goes out of scope.

    restart()
        *stop()* and *start()* R.

    bin()
        Get or set the path to the R executable.

    version()
        Get the version number of R.

    is_shared()
        Was R started in shared mode?

    is_started()
        Is R running?

    pid()
        Return the PID of the running R process

INSTALLATION
    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:

    IPC::Run
    Regexp::Common
    Text::Balanced (>= 1.97)
    Text::Wrap
    version (>= 0.77)

SEE ALSO
    *   Statistics::R::Win32

    *   Statistics::R::Legacy

    *   The R-project web site: <http://www.r-project.org/>

    *   Statistics::* modules for Perl:
        <http://search.cpan.org/search?query=Statistics&mode=module>

AUTHORS
    Florent Angly <florent.angly@gmail.com> (2011 rewrite)

    Graciliano M. P. <gm@virtuasites.com.br> (original code)

MAINTAINERS
    Florent Angly <florent.angly@gmail.com>

    Brian Cassidy <bricas@cpan.org>

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

BUGS
    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

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