--------------------------- -- ChangeLog - abn -- --------------------------- 2023-05-06 Matteo Delucchi (version 2.7-5) * Changed contributors * Fixed unicode-character issue in NAMESPACE 2023-01-21 Reinhard Furrer (version 2.7-4) * Changes for JSS article. * Minor internal improvements (eliminated tests based on `class()`) 2022-06-15 Reinhard Furrer (version 2.7-3, 2.7-1) * Fixed a bug in `buildScoreCache.mle()` () * Eliminated a couple potential warnings. * Improvement of version `abn.Version()` * Cleaned control arguments * Improved a few man pages 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