CVS commit: wip/R-bnlearn

["Mike M. Volokhov" <bubuchka%users.sourceforge.net@localhost>]

Module name:    wip
Committed by:   bubuchka
Date:           Wed Oct  9 14:20:22 UTC 2013

Modified Files:
        wip/R-bnlearn: Makefile distinfo

Log Message:
Update bnlearn to version 3.4. Major changes:

  * move the test counter into bnlearn's namespace.
  * include Tsamardinos' optimizations in mmpc(..., optimized = FALSE),
     but not backtracking, to make it comparable with other learning
     algorithms.
  * check whether the residuals and the fitted values are present before
     trying to plot a bn.fit{,.gnode} object.
  * fixed two integer overflows in factors' levels and degrees of freedom
     in large networks.
  * added {compelled,reversible}.arcs().
  * added the MSE and predictive correlation loss functions to bn.cv().
  * use the unbiased estimate of residual variance to compute the standard
     error in bn.fit(..., method = "mle") (thanks Jean-Baptiste Denis).
  * revised optimizations in constraint-based algorithms, removing most
     false positives by sacrificing speed.
  * fixed warning in cp{dist,query}().
  * added support for ordered factors.
  * implemented the Jonckheere-Terpstra test to support ordered factors
     in constraint-based structure learning.
  * added a plot() method for bn.strength objects containing bootstrapped
     confidence estimates; it prints their ECDF and the estimated 
     significance threshold.
  * fixed dimension reduction in cpdist().
  * reimplemented Gaussian rbn() in C, it's now twice as fast.
  * improve precision and robustness of (partial) correlations.
  * remove the old network scripts for network that are now available from
     www.bnlearn.com/bnrepository.
  * implemented likelihood weighting in cp{dist,query}().


To generate a diff of this commit:
cvs -z3 rdiff -u -r1.11 -r1.12 wip/R-bnlearn/Makefile
cvs -z3 rdiff -u -r1.5 -r1.6 wip/R-bnlearn/distinfo

To view a diff of this commit:
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/R-bnlearn/Makefile?r1=1.11&r2=1.12
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/R-bnlearn/distinfo?r1=1.5&r2=1.6

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

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