RNetica is best thought of as a "glue" layer between the open source statistical programing language R http://www.r-project.org/ and the proprietary Bayesian network engine Netica ® http://www.norsys.com/. Although there are some minor extensions to the Netica API, the primary purpose of RNetica is to provide a binding for the Netica API functions inside of R.
There are two big advantages to this. One is that while the Netica GUI is helpful for model development, entering evidence by point and click is cumbersome for real work. Embedding the Netica API within R means that R can be used for data preparation and cleaning, the data can be entered into a model developed with the Netica GUI and the results extracted and graphed using the graphical power of R. The second big advantage is that R is an interpreted language, which supports rapid improvisation of code. This make it substantially faster to work in RNetica than using the C or Java APIs.
The 0.3 series of releases includes a number of different improvements.
gctorture(TRUE), which should mean that is it is much more robust to memory errors. This is still a beta version, caution is still advisable.
Known issues with this release.
Approximately 4/5 of the API functionality is mapped. Things that are still not mapped:
There are three layers to the complete RNetica environment, each with their own licensing terms.
Once you have obtained a license key from Norsys, you can use it in
one of two ways. First, it can be passed as an argument to the
StartNetica(license key) (you may need to
StopNetica() first). Second, if you execute the
NeticaLicenseKey <- license key in the
main R workspace (the default namespace), then RNetica will use that
value when loaded through
Without the license key, the Netica API operates in a limited mode. All of the functions in the test scripts will run, but the size of the networks is generally limited.
The current version (0.4-1) incorporates approximately 75% of the Netica C API Version 5.04 (no new version since 2012). This is sufficient functionality to build, compile and carry out inferences with a Bayesian network. Some of the more advanced functionality, including support for databases, influence diagrams, and dynamic Bayesian networks is not yet developed.
Although an extensive test script exists for RNetica (most of this is exposed on the manual pages), the testing away from these simple tests has been particularly light. In particular, I have not yet used valgrind to test for memory leaks. It is currently a beta release. Note that because it uses calls to C code, it is possible for RNetica to crash R. Plan your work accordingly.
The development has been with R version 3.0.1 under Ubuntu
14.04 with Netica API 5.04.
R CMD check RNetica
runs under Mac OS X and Windows 7 without errors. Almost all of the
testing has been with the 64 bit versions of R and Netica. There may
be some problems that crop up under 32 bit versions.
Version 0.2-7 was developed and tested under R 2.15.2. The windows binary for that version is a R 2.15 binary.
The following releases are archived here:
|0.1-8||RNetica_0.1-8.tar.gz||First reasonably functional version.|
|0.2-5||RNetica_0.2-5.tar.gz||Initial version used for Newton's Playground|
|0.2-6||RNetica_0.2-6.tar.gz||RNetica-manual_0.2-6.pdf||Fixed Windows installation.|
|0.2-7||RNetica_0.2-7.tar.gz||RNetica_0.2-7.zip||RNetica_0.2-7.tgz||RNetica-manual_0.2-7.pdf||Last Version for R 2.15|
|0.3-1||RNetica_0.3-1.tar.gz||RNetica-manual_0.3-1.pdf||R 3.0: Added NodeExperience and Case Writing (not Reading)|
|0.3-3||RNetica_0.3-3.tar.gz||RNetica_0.3-3.zip||RNetica_0.3-3.tgz||RNetica-manual_0.3-3.pdf||R 3.0: Support for Case Streams (file and memory)|
|0.4-1||RNetica_0.4-1.tar.gz||RNetica_0.4-1.zip||RNetica_0.4-1.tgz||RNetica-manual_0.4-1.pdf||Equations, Decisions, Continuous Nodes and Mutual Information|
|0.4-2||RNetica_0.4-2.tar.gz||RNetica_0.4-2.zip||RNetica_0.4-2.tgz||RNetica-manual_0.4-2.pdf||Random Findings Generation, as.IDname() cleanup, bug fixes|
|0.4-4||RNetica_0.4-4.tar.gz||RNetica_0.4-4.zip||RNetica_0.4-4.tgz||RNetica-manual_0.4-4.pdf||Peanut compatability, User Object support||0.4-5||RNetica_0.4-5.tar.gz||RNetica_0.4-5.zip||RNetica_0.4-5.tgz||RNetica-manual_0.4-5.pdf||Peanut compatability, User Object support|
Note the source versions have been compiled and tested under Linux/Unix, Mac OS X and Windows. Note that for Windows and Mac OS X, compiling source packages requires the R development kit to be installed. See the appropriate R FAQ for your operating system. You should also be familiar with building R packages, see the Writing R Extensions manual.
Compiling from sources requires that you have already downloaded and unpacked the Netica C API from Norsys. Under *nix (including Mac OS X) the location of the library can be passed to the configure command, e.g.:
R CMD INSTALL RNetica --configure-args='--with-netica=/Users/ralmond/software/Netica_API_504/'
Under Windows (or as an alternative to the
switch), the environmental variable
NETICA_HOME can be
set to the location in which the Netica API was unpacked. I have only
tested with the API version 5.04, not with earlier versions.
Although I am now supplying Windows and Mac OS X binaries, which include the Netica API (currently version 5.04). As this is still an early test release, it will help you to have a local R guru to ask support questions, and help file bug reports if needed. NOTE: this is an unlicensed version of the API: you still need to purchase a license (although the unlicensed version will run the sample code in the man pages).
A recent communication with Brent indicated that a new Netica API will be out soon. When that comes out, there will likely be a big update.
The latest development version is available as a subversion repository at: https://pluto.coe.fsu.edu/svn/common/RNetica/.
If you have patches or other correspondence about RNetica you can contact me at firstname.lastname@example.org. If you are filing a bug report, please be sure to include the following information:
Netica and Norsys are registered trademarks of Norsys, LLC, used by permission.
Although Norsys has been generally supportive of the RNetica project, they do not offer formal support in any way. (In particular, the do not currently have anybody on staff who knows R.) All support requests should be sent to the package maintainers.
The software is offered AS IS, without any warranty of any kind. Support is provided on a volunteer basis, and may not be immediately forthcoming.