---------------------------
-- ChangeLog - abn --
---------------------------
2023-09-01 Matteo Delucchi (version 3.0.0)
  * Implemented random-intercept model for `method="mle"` with argument `group.var`.
  * simulateAbn(): Fixed to run with all arguments. Enhancement: Simulates a hierarchical model if `group.var` is provided.
  * Fixed parallel computing for `method="mle"` that did not always run smoothly.
  * Beware, the structure of some objects has changed!
  * Updated documentation to Roxygen.
  * Rigorous checking of function arguments.
  * Upgraded unit test for testthat e3.
  * Implemented extensive unit tests and CI/CD pipelines.
  * Many (!) bugs fixed that mainly flew under the radar.
  * Removed deprecated functions.
  * Refactoring here and there. Especially to harmonise `buildScoreCache()` and `fitAbn()` for both methods "mle" and "bayes".

2022-04-02 Reinhard Furrer  (version 2.7-0)

  * plotAbn(): new arguments, now fully based on class `graphAM`, proper handling of lty, lwd etc.
  * options of `fitAbn()` and `buildScoreCache()` are now handled with a list passed to argument `control=`. Some of the default values have been slightly adapted.
  * Default list available via `fit.control()` and `build.control()`, including more options!
  * Significantly improved help of several functions and examples.
  * Improved display of print methods.
  * Possiblity to use single threaded with `for()` loop and with `foreach()`.
  * Due to proper method handling, the arguments `create.graph` in `searchHillClimber()` and `fitAbn(method="bayes")` has been removed.
  * Argument `verbose` properly implemented (including passing to JAGS functions).
  * New function `compareEG()` to compare two essential graphs.
  * Additional argument checking an cleaning of many error messages.


  * Internal changes:
	Option `error.verbose` properly propagated to C functions.
	New option `trace` passed to "lbfgsb".
	Less ARMA messages, using now `#define ARMA_WARN_LEVEL 1`.
	Some GSL error now caught at R level.
	Severe R and moderate C code cleaning.



2021-06-08 Gilles Kratzer, Reinhard Furrer & Kalina Cherneva (version 2.6.0)
	   * Bug fixes:
	      . initial values for several chains in `simulateAbn()`
	      . new default value for `method` in `fitAbn()`
	      . new default value `method='bic'` in `mostProbable()`
	      . minor bug fixes in `plotAbn()`
	      . minor bug fix in `help(plotAbn)`
	      . number of parent specification for `buildScoreCache( , method='mle')`
	   * Renaming many function arguments for consistency
	   * Reordering, purging and adding function argments
	   * Parallelization of `buildScoreCache(, method='mle')`
	   * Cleaning of RCpp with improved default parameters (speed up 5%)
	   * Adapting authorship of package
	   * Minor cleaning of `Examples` in the help files


2021-04-23 Gilles Kratzer & Reinhard Furrer (version 2.5.0)
	   * Renaming many functions to CamelCase for consistency
	   * Renaming many arguments for consistency
	   * Reordering, purging and adding function argments
	   * Major changes in `plotAbn()`
	   * Cleaning of several help files

2020-10-31 Gilles Kratzer & Reinhard Furrer (version 2.4.0)
	   * Update on citations
	   * Update on ORCID number

2020-10-22 Gilles Kratzer & Reinhard Furrer (version 2.3.0)
	   * Requirement for use of R>=4.0.0

2020-06-13 Gilles Kratzer & Reinhard Furrer (version 2.2.1)
	   * Patch for S4 exports not stated in the package
	   * Testing automatic (testhat.R in tests repository)
	   * Updated version of the vignette

2019-11-22 Gilles Kratzer & Reinhard Furrer (version 2.2)
	   * New vignette describing new functionalities!
	   * Old vignette is store in the﻿ directories inst/bootstrapping_example and inst/old_vignette
	   * Dataset: FCV
	   * Methods related to the class abnFit: family, logLik, AIC, BIC, nobs, coef
	   * Bugs corrected in plotabn()
	   * Compilation warnings corrected
	   * Typos in man help files corrected
	   * Compiler flags that were not compatible with the Solaris OS

2019-07-04 Gilles Kratzer & Reinhard Furrer (version 2.1)
	   * Compiler flags that were not compatible with the Solaris system
	   * Note related to INLA

2019-07-01 Gilles Kratzer & Reinhard Furrer (version 2.0)
	   * Implementation of S3 methods (print, summary, plot)
	   * New classes:
	   		* abnDag, abnCache, abnHeuristic, abnMostprobable, abnHillClimber, abnFit
	   * renaming of functions
	   		* link.strength() -> linkStrength()
	   		* search.heuristic() -> searchHeuristic()
	   		* backward compatibility is not ensured for those functions
	   * New tests implemented for internal validation and some backward compatibility
	   * Dependence with Cairo removed
	   * modification of search.hillclimber(): no interactive plotting possible
	   * buildscorecache() becomes a parametrisable wrapper for the bayesian and the mle methods
	   * fitabn() becomes a parametrisable wrapper for the bayesian and the mle methods
	   * Dataset: adg
	   * Multiple Bugs corrected

2018-07-23 Gilles Kratzer (version 1.2)
	   * (many) new functions
	   * buildscorecache.mle()
	   * fitabn.mle()
	   * plotabn()
	   * simulateabn()
	   * expit(), logit(), odds() and or()
	   * mb()
	   * link.strength()
	   * discretization()
	   * essentialGraph()
	   * compareDag()
	   * infoDag()
	   * simulateDag()
	   * search.heuristic()
	   * entropyData()
	   * miData()

	   * modification of existing functions:
	   * mostprobable()

2016-11-09 Gilles Kratzer (version 1.0.2)
	   * Default ban and retain matrix
	   * Automatic testing procedure of the package

2016-01-11 Pittavino Marta (version 1.0)
	   New vignette uploaded.

2015-12-22 Pittavino Marta (version 0.86)
	   INLA routine updated, ERROR and NOTE addressed.

2014-12-22 Pittavino Marta (version 0.85)
	   * Published Version v0.85 on CRAN

2014-12-09 Pittavino Marta (version 0.85)
           * cleanup file to delete additional Makevars added

2014-12-08 Pittavino Marta (version 0.85)
           * FOSS license --as-cran NOTE addressed, eliminated BuildVignettes NO in the DESCRIPTION file

2014-12-06 Pittavino Marta (version 0.84)
           * v0.84 submitted to CRAN

2014-12-05 Pittavino Marta (version 0.84)
           * dependencies --as-cran NOTE addressed, with .Rprofile
           * graphical issue with Sweave solved

2014-12-04 Pittavino Marta (version 0.84)
           * finished to edit vignette

2014-11-23/24 Pittavino Marta (version 0.84)
              * updating the vignette

2014-11-03/04 Pittavino Marta (version 0.84)
              * issue with Rd2pdf and LaTeX addressed

2014-10-27 Pittavino Marta (version 0.84)
           * installation of local version of abn to text and work with vignette

2014-10-23 Pittavino Marta (version 0.84)
           * confirmation of the change of maintainer

2014-10-13 Pittavino Marta (version 0.84)
           * updated Rclean for file .log and .status
           * check length characters in manual

2014-10-06 Pittavino Marta (version 0.84)
           * compressed Data with resaveRdaFiles(,compress=c("xz"))
           * solved installing issue (Rclean update)

2014-10-03 Pittavino Marta (version 0.84)
	       * alias Rclean extended
	       * eliminate old and very old version
	       * comment out require(Cairo) line-code

2014-10-02 Reinhard Furrer (version 0.84)
	       * Cairo NOTE fixed, moved from Suggests to Depends
	       * DESCRIPTION and NAMESPACE update
           * check if last amendments works
	       * .gitignore create

2014-09-29 Pittavino Marta (version 0.84)
	       * update version
	       * rename R function as the one in manual

2014-09-26 Pittavino Marta (version 0.83)
	       * update DESCRIPTION

2014-09-19 Pittavino Marta (version 0.83)
 	       * update DESCRIPTION
           * update tographviz documentation
           * create ChangeLog file
