./wip/R-bnlearn, Bayesian network structure learning, parameter learning and inference

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Branch: CURRENT, Version: 4.0nb1, Package name: R-bnlearn-4.0nb1, Maintainer: mishka

Bayesian network structure learning, parameter learning and inference.

This package implements constraint-based (GS, IAMB, Inter-IAMB,
Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu),
score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and
RSMAX2) structure learning algorithms for discrete, Gaussian and
conditional Gaussian networks, along with many score functions and
conditional independence tests. The Naive Bayes and the Tree-Augmented
Naive Bayes (TAN) classifiers are also implemented.

Some utility functions (model comparison and manipulation, random
data generation, arc orientation testing, simple and advanced plots)
are included, as well as support for parameter estimation (maximum
likelihood and Bayesian) and inference, conditional probability
queries and cross-validation.

Required to run:
[lang/g95] [math/R] [math/blas]

Required to build:

Master sites: (Expand)

Version history: (Expand)

CVS history: (Expand)

   2015-03-02 15:31:25 by Mike M. Volokhov | Files touched by this commit (3)
Log message:
Update R-bnlearn to version 3.7.1.


bnlearn (3.7.1)

  * small changes to make CRAN check happy.

bnlearn (3.7)

  * fixed the default setting for the number of particles in cpquery()
     (thanks Nishanth Upadhyaya).
  * reimplemented common test patterns in monolithic C functions to speed
     up constraint-based algorithms.
  * added support for conditional linear Gaussian (CLG) networks.
  * fixed several recursion bugs in choose.direction().
  * make read.{bif,dsc,net}() consistent with the `$<-` method for bn.fit
     objects (thanks Felix Rios).
  * support empty networks in read.{bif,dsc,net}().
  * fixed bug in hc(), triggered when using both random restarts and the
     maxp argument (thanks Irene Kaplow).
  * correctly initialize the Castelo & Siebes prior (thanks Irene Kaplow).
  * change the prior distribution for the training variable in classifiers
     from the uniform prior to the fitted distribution in the
     bn.fit.{naive,tan} object, for consistency with gRain and e1071 (thanks
     Bojan Mihaljevic).
  * note AIC and BIC scaling in the documentation (thanks Thomas Lefevre).
  * note limitations of {white,black}lists in tree.bayes() (thanks Bojan
  * better input sanitization in custom.fit() and bn.fit<-().
  * fixed .Call stack imbalance in random restarts (thanks James Jensen).
  * note limitations of predict()ing from bn objects (thanks Florian Sieck).

bnlearn (3.6)

  * support rectangular nodes in {graphviz,strength}.plot().
  * fixed bug in hc(), random restarts occasionally introduced cycles in
     the graph (thanks Boris Freydin).
  * handle ordinal networks in as.grain(), treat variables as categorical
     (thanks Yannis Haralambous).
  * discretize() returns unordered factors for backward compatibility.
  * added write.dot() to export network structures as DOT files.
  * added mutual information and X^2 tests with adjusted degrees of freedom.
  * default vstruct() and cpdag() to moral = FALSE (thanks Jean-Baptiste
  * implemented posterior predictions in predict() using likelihood weighting.
  * prevent silent reuse of AIC penalization coefficient when computing BIC
     and vice versa (thanks MarГ­a Luisa Matey).
  * added a "bn.cpdist" class and a "method" attribute to \ 
the random data
     generated by cpdist().
  * attach the weights to the return value of cpdist(..., method = "lw").
  * changed the default number of simulations in cp{query, dist}().
  * support interval and multiple-valued evidence for likelihood weighting
     in cp{query,dist}().
  * implemented dedup() to pre-process continuous data.
  * fixed a scalability bug in blacklist sanitization (thanks Dong Yeon Cho).
  * fixed permutation test support in relevant().
  * reimplemented the conditional.test() backend completely in C for
     speed, it is now called indep.test().
   2013-10-09 16:20:22 by Mike M. Volokhov | Files touched by this commit (2)
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
  * 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
  * implemented likelihood weighting in cp{dist,query}().
   2013-03-29 14:12:00 by Mike M. Volokhov | Files touched by this commit (2)
Log message:
Update R-bnlearn to version 3.3.  Major changes:

  * fixed cpdag() and cextend(), which returned an error about
     the input graph being cyclic when it included the CPDAG of
     a shielded collider (thanks Jean-Baptiste Denis).
  * do not generate observations from redundant variables (those
     not in the upper closure of event and evidence) in cpdag()
     and cpquery().
  * added Pena's relevant() nodes identification.
  * make custom.fit() robust against floating point errors
     (thanks Jean-Baptiste Denis).
  * check v-structures do not introduce directed cycles in the
     graph when applying them (thanks Jean-Baptiste Denis).
  * fixed a buffer overflow in cextend() (thanks Jean-Baptiste
  * added a "strict" argument to cextend().
  * removed Depends on the graph package, which is in Suggests
     once more.
  * prefer the parallel package to snow, if it is available.
  * replace NaNs in bn.fit objects with uniform conditional
     probabilities when calling as.grain(), with a warning
     instead of an error.
  * remove reserved characters from levels in write.{dsc,bif,net}().
  * fix the Gaussian mutual information test (thanks Alex Lenkoski).
   2013-03-19 02:22:55 by Mike M. Volokhov | Files touched by this commit (17)
Log message:
Move LICENSE right below COMMENT, that's where it usually should be.
Noted by <wiz> - thank you very much!
   2012-11-16 02:05:42 by Mike M. Volokhov | Files touched by this commit (3)
Log message:
Update R-bnlearn to version 3.1. Major changes:

* fixed all.equal(), it did not work as expected on networks
  that were idetical save for the order of nodes or arcs.
* added a "moral" argument to cpdag() and vstructs() to make
  those functions follow the different definitions of v-structure.
* added support for graphs with 1 and 2 nodes.
* fixed cpquery() handling of TRUE (this time for real).
* handle more corner cases in dsep().
* added a BIC method for bn and bn.fit objects.
* added the semiparametric tests from Tsamardinos & Borboudakis
  (thanks Maxime Gasse).
* added posterior probabilities to the predictions for
  {naive,tree}.bayes() models.
* fixed buffer overflow in rbn() for discrete data.
   2012-08-30 21:03:42 by Mike M. Volokhov | Files touched by this commit (10)
Log message:
Cleanup Makefiles and get them ready to import.
   2012-08-29 23:40:37 by Mike M. Volokhov | Files touched by this commit (1)
Log message:
Author provides a perfect overview in the package description. Sync to it.
   2012-08-28 17:39:17 by Mike M. Volokhov | Files touched by this commit (6)
Log message:
Fix spacing.