oracular (3) Statistics::R::IO.3pm.gz
NAME
Statistics::R::IO - Perl interface to serialized R data
VERSION
version 1.0002
SYNOPSIS
use Statistics::R::IO;
my $var = Statistics::R::IO::readRDS('file.rds');
print $var->to_pl;
my %r_workspace = Statistics::R::IO::readRData('.RData');
while (my ($var_name, $value) = each %r_workspace) {
print $var_name, $value;
}
my $pi = Statistics::R::IO::evalRserve('pi');
print $pi->to_pl;
DESCRIPTION
This module is a pure-Perl implementation for reading native data files produced by the R statistical
computing environment <http://www.r-project.org>)
It provides routines for reading files in the two primary file formats used in R for serializing native
objects:
RDS RDS files store a serialization of a single R object (and, if the object contains references to other
objects, such as environments, all the referenced objects as well). These files are created in R
using the "readRDS" function and are typically named with the ".rds" file extension.
RData
RData files store a serialization of a collection of named objects, typically a workspace. These
files are created in R using the "save" function and are typically named with the ".RData" file
extension. (Contents of the R workspace can also be saved automatically on exit to the file named
.RData, which is by default automatically read in on startup.)
As of version 0.04, the module can also evaluate R code on a remote host that runs the Rserve
<http://www.rforge.net/Rserve/> binary R server. This allows Perl programs to access all facilities of R
without the need to have a local install of R or link to an R library.
See "SUBROUTINES" for invocation and usage information on individual subroutines, and the R Internals
manual <http://cran.r-project.org/doc/manuals/R-ints.html> for the specification of the file formats.
EXPORT
Nothing by default. Optionally, subroutines "readRDS", "readRData", and "evalRserve", or ":all" for all
three.
SUBROUTINES
readRDS EXPR
Reads a file in RDS format whose filename is given by EXPR and returns a Statistics::R::REXP object.
readRData EXPR
Reads a file in RData format whose filename is given by EXPR and returns a hash whose keys are the
names of objects stored in the file with corresponding values as Statistics::R::REXP instances.
evalRserve REXPR [ HOSTNAME [, PORT] | HANDLE]
Evaluates an R expression, given as text string in REXPR, on an Rserve
<http://www.rforge.net/Rserve/> server and returns its result as a Statistics::R::REXP object.
The server location can be specified either by its host name and (optionally) port or by a connected
instance of IO::Handle. The caller passing the HANDLE is responsible for reading (and checking) the
server ID that is returned in the first 32-byte response when the connection was established. This
allows opening the connection once and reusing it in multiple calls to 'evalRserve'.
If only REXPR is given, the function assumes that the server runs on the localhost. If PORT is not
specified, it defaults to the standard Rserve port, 6311.
The function will close the connection to the Rserve host if it has opened it itself, but not if the
connection was passed as a HANDLE.
DEPENDENCIES
Requires perl 5.010 or newer.
Core modules
• strict
• warnings
• overload
• Carp
• Exporter
• Module::Build
• Scalar::Util
• Test::More
Additional CPAN modules
• Class::Tiny
• Class::Tiny::Antlers
• Class::Method::Modifiers
• namespace::clean
• Test::Fatal
BUGS AND LIMITATIONS
The module currently handles the 'version 2' serialization format, used since R 1.4.0 (released in
December 2001). Only XDR and native-order binary is implemented, and since the R documentation describes
the ASCII save format as "now mainly of historical interest", this is unlikely to change soon. No check
is performed that a file stored in native-order binary was created on a platform that used the same
order, and it is up to the caller to ensure compatibility. (Given that the default save format is XDR,
and the prevalence of Intel platforms, this is unlikely to be a problem for either publicly-distributed
or internal data files.)
Data files compressed with 'gzip' and 'bzip2' are supported, but not 'xz' ones. Again, given the R
defaults ('gzip') and the fact that "IO::Uncompress::UnXz" is not production-ready, this is unlikely to
change soon.
There are some R types that are not (yet) implemented, although all typical "user-facing" types -- such
as vectors, lists, and environments -- are. The remaining R types will be implemented as-needed; in other
words, if you come across one that you need to read a particular file, please send me the type (the id
will included in the "unimplemented SEXPTYPE" error message) and, if possible, how it was generated.
There are no known bugs in this module. Please report any bugs or feature requests to
"bug-statistics-r-io at rt.cpan.org", or through the web interface at
<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Statistics-R-IO>. I will be notified, and then you'll
automatically be notified of progress on your bug as I make changes.
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc Statistics::R::IO
You can also look for information at:
• RT: CPAN's request tracker (report bugs here)
<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Statistics-R-IO>
• AnnoCPAN: Annotated CPAN documentation
<http://annocpan.org/dist/Statistics-R-IO>
• CPAN Ratings
<http://cpanratings.perl.org/d/Statistics-R-IO>
• Search CPAN
<http://search.cpan.org/dist/Statistics-R-IO/>
AUTHOR
Davor Cubranic <cubranic@stat.ubc.ca>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2017 by University of British Columbia.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007