R.matlab-package: Package R.matlab
In R.matlab: Read and Write MAT Files and Call MATLAB from Within R
R.matlab-package R Documentation
Package R.matlab
Description
Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
In brief, this package provides a one-directional interface from
R to MATLAB, with communication taking place via a TCP/IP connection
and with data transferred either through another connection or via
the file system. On the MATLAB side, the TCP/IP connection is handled
by a small Java add-on.
The methods for reading and writing MAT files are stable.
The R to MATLAB interface, that is the Matlab class, is less
prioritized and should be considered a beta version.
For package history, see showHistory(R.matlab).
Requirements
This is a cross-platform package implemented in plain R.
This package depends on the R.oo package [1].
To use the Matlab class or requesting verbose output messages, the
R.utils package is loaded
when needed (and therefore required in those cases).
The readMat() and writeMat() methods do not
require a MATLAB installation neither do they depend on the
Matlab class.
To connect to MATLAB, MATLAB v6 or higher is required.
It does not work with MATLAB v5 or before (because those
versions do not support Java).
For confirmed MATLAB versions, see the Matlab class.
Installation
To install this package do
install.packages("R.matlab")
To get started
To get started, see:
-
readMat() and writeMat() - For reading and writing
MAT files (MATLAB is not needed).
-
Matlab - To start MATLAB and communicate with it from R.
Miscellaneous
A related initiative is RMatlab by Duncan Temple Lang
and Omegahat. It provides a bi-directional interface between the
R and MATLAB languages. For more details, see
https://www.omegahat.net/RMatlab/.
To call R from MATLAB on Windows (only), see MATLAB R-link
by Robert Henson available at the MATLAB Central File Exchange
(https://www.mathworks.com/matlabcentral/fileexchange/5051-matlab-r-link).
How to cite this package
Whenever using this package, please cite as
Troubleshooting
In general:
For trouble shooting in general, rerun erroneous function with
verbose/debug messages turned on. For readMat() and writeMat()
see their help. For communication with a MATLAB server, use
matlab <- Matlab()
setVerbose(matlab, threshold = -2)
The lower the threshold is the more information you will see.
Cannot connect to MATLAB:
If R fails to connect to MATLAB, make sure to try the example in
help(Matlab) first. Make sure that the MATLAB server is running
before trying to connect to it from R first. If MATLAB is running
but open() times out, make sure MATLAB is listening to the
same port that R is trying to connect to. If that does not help,
try to increase the time-out limit, see help(open.Matlab).
Expected an 'answer' from MATLAB, but kept receiving nothing.:
When launching a really long MATLAB process by evaluate(), you
may get the above error message.
Reason: This happens because evaluate() expect a reply
from MATLAB as soon as MATLAB is done. The waiting should be "blocked",
i.e. it should wait until it receives something. For unknown reasons,
this is not always happening. The workaround we have implemented is to
try readResult/maxTries waiting readResult/interval seconds
in-between.
Solution:
Increase the total waiting time by setting the above options, e.g.
setOption(matlab, "readResult/interval", 10) # Default is 1 second
setOption(matlab, "readResult/maxTries", 30 * (60 / 10)) # ~30 minutes
Wishlist
Here is a list of features that would be useful, but which I have
too little time to add myself. Contributions are appreciated.
Add a function, say, Matlab$createShortcut() which
creates a Windows shortcut to start the MATLAB server
by double clicking it. It should be possible to create
it in the current directory or to the Desktop.
Maybe it is possible to do this upon installation and
even to a Start -> All Programs -> R menu.
To improve security, update the MatlabServer.m script to
allow the user to specify a "password" to be send upon
connection from R in order for MATLAB to accept the
connection. This password should be possible to specify
from the command line when starting MATLAB. If not given,
no password is required.
Add additional methods to the Matlab class. For instance,
inline function in MATLAB could have its own method.
Wrap up common MATLAB commands as methods of the Matlab
class, e.g. who(matlab), clear(matlab) etc.
Can this be done automatically using "reflection", so
that required arguments are automatically detected?
Add access to MATLAB variables via "$" and
"$<-", e.g. matlab$A and
matlab$A <- 1234. Is this wanted?
Maybe the same for functions, e.g. matlab$dice(1000).
Is it possible to return multiple return values?
If you consider implement some of the above, make sure it is not
already implemented by downloading the latest "devel" version!
Acknowledgments
Thanks to the following people who contributed with valuable
feedback, suggestions, code and more:
Patrick Drechsler, Biocenter, University of Wuerzburg.
Spencer Graves.
Andy Jacobson, Atmospheric and Oceanic Sciences Program,
Princeton University.
Jason Riedy, Computer Science Division,
University of California, Berkeley.
Chris Sims, Department of Economics, Princeton University.
Frank Stephen, National Renewable Energy Laboratory.
Yichun Wei, Department of Biological Sciences,
University of Southern California.
Wang Yu, ECE Department, Iowa State University.
License
The releases of this package is licensed under
LGPL version 2.1 or newer.
The development code of the packages is under a private license
(where applicable) and patches sent to the author fall under the
latter license, but will be, if incorporated, released under the
"release" license above.
References
[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/
Author(s)
Henrik Bengtsson
R.matlab documentation built on Aug. 26, 2022, 1:07 a.m.
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| R.matlab-package | R Documentation |
Package R.matlab
Description
Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
In brief, this package provides a one-directional interface from R to MATLAB, with communication taking place via a TCP/IP connection and with data transferred either through another connection or via the file system. On the MATLAB side, the TCP/IP connection is handled by a small Java add-on.
The methods for reading and writing MAT files are stable. The R to MATLAB interface, that is the Matlab class, is less prioritized and should be considered a beta version.
For package history, see showHistory(R.matlab).
Requirements
This is a cross-platform package implemented in plain R. This package depends on the R.oo package [1].
To use the Matlab class or requesting verbose output messages, the R.utils package is loaded when needed (and therefore required in those cases).
The readMat() and writeMat() methods do not
require a MATLAB installation neither do they depend on the
Matlab class.
To connect to MATLAB, MATLAB v6 or higher is required.
It does not work with MATLAB v5 or before (because those
versions do not support Java).
For confirmed MATLAB versions, see the Matlab class.
Installation
To install this package do
install.packages("R.matlab")
To get started
To get started, see:
-
readMat() andwriteMat() - For reading and writing MAT files (MATLAB is not needed). -
Matlab- To start MATLAB and communicate with it from R.
Miscellaneous
A related initiative is RMatlab by Duncan Temple Lang and Omegahat. It provides a bi-directional interface between the R and MATLAB languages. For more details, see https://www.omegahat.net/RMatlab/. To call R from MATLAB on Windows (only), see MATLAB R-link by Robert Henson available at the MATLAB Central File Exchange (https://www.mathworks.com/matlabcentral/fileexchange/5051-matlab-r-link).
How to cite this package
Whenever using this package, please cite as
Troubleshooting
In general:
For trouble shooting in general, rerun erroneous function with
verbose/debug messages turned on. For readMat() and writeMat()
see their help. For communication with a MATLAB server, use
matlab <- Matlab() setVerbose(matlab, threshold = -2)
The lower the threshold is the more information you will see.
Cannot connect to MATLAB:
If R fails to connect to MATLAB, make sure to try the example in
help(Matlab) first. Make sure that the MATLAB server is running
before trying to connect to it from R first. If MATLAB is running
but open() times out, make sure MATLAB is listening to the
same port that R is trying to connect to. If that does not help,
try to increase the time-out limit, see help(open.Matlab).
Expected an 'answer' from MATLAB, but kept receiving nothing.:
When launching a really long MATLAB process by evaluate(), you
may get the above error message.
Reason: This happens because evaluate() expect a reply
from MATLAB as soon as MATLAB is done. The waiting should be "blocked",
i.e. it should wait until it receives something. For unknown reasons,
this is not always happening. The workaround we have implemented is to
try readResult/maxTries waiting readResult/interval seconds
in-between.
Solution:
Increase the total waiting time by setting the above options, e.g.
setOption(matlab, "readResult/interval", 10) # Default is 1 second setOption(matlab, "readResult/maxTries", 30 * (60 / 10)) # ~30 minutes
Wishlist
Here is a list of features that would be useful, but which I have too little time to add myself. Contributions are appreciated.
Add a function, say,
Matlab$createShortcut()which creates a Windows shortcut to start the MATLAB server by double clicking it. It should be possible to create it in the current directory or to the Desktop. Maybe it is possible to do this upon installation and even to a Start -> All Programs -> R menu.To improve security, update the MatlabServer.m script to allow the user to specify a "password" to be send upon connection from R in order for MATLAB to accept the connection. This password should be possible to specify from the command line when starting MATLAB. If not given, no password is required.
Add additional methods to the Matlab class. For instance, inline function in MATLAB could have its own method.
Wrap up common MATLAB commands as methods of the Matlab class, e.g.
who(matlab),clear(matlab)etc. Can this be done automatically using "reflection", so that required arguments are automatically detected?Add access to MATLAB variables via
"$"and"$<-", e.g.matlab$Aandmatlab$A <- 1234. Is this wanted? Maybe the same for functions, e.g.matlab$dice(1000). Is it possible to return multiple return values?
If you consider implement some of the above, make sure it is not already implemented by downloading the latest "devel" version!
Acknowledgments
Thanks to the following people who contributed with valuable feedback, suggestions, code and more:
Patrick Drechsler, Biocenter, University of Wuerzburg.
Spencer Graves.
Andy Jacobson, Atmospheric and Oceanic Sciences Program, Princeton University.
Jason Riedy, Computer Science Division, University of California, Berkeley.
Chris Sims, Department of Economics, Princeton University.
Frank Stephen, National Renewable Energy Laboratory.
Yichun Wei, Department of Biological Sciences, University of Southern California.
Wang Yu, ECE Department, Iowa State University.
License
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private license (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
References
[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/
Author(s)
Henrik Bengtsson
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