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Changelog

Source: NEWS.md

abn 3.0.7

2024-03-27 Matteo Delucchi

  • Reduced package size by compressions.
  • Speed up the checks on CRAN by reducing the number of examples to be run.
  • Fixed the checks on CRAN by resetting user options within functions and examples.
  • Fixed failing tests on CRAN due to the use of INLA package.
  • Reduced the number of empty tests by gracefully handling the specific conditions.
  • Improved documentation, fixed typos and added return values for each function.
  • Added Jonas Liechti as a contributor.

abn 3.0.6

CRAN release: 2024-03-22

2024-03-21 Matteo Delucchi

  • New website
  • added JOSS paper
  • Changed ChangeLog into NEWS.md
  • Revised CITATION file
  • Updated README
  • added logo
  • Revised class names and methods
  • Added functional test for getmarginals()
  • Check for validity and sensibility of the compute.fixed argument.
  • Check for validity and sensibility of the check argument in buildscoreCache().
  • Check codecoverage
  • harmonised plotting across different classes
  • Created new vignettes
  • relaxed tests to allow for complete and partial scientific notation in string outputs from BUGS files.
  • avoid examples and tests on CRAN that require INLA
  • Restructured the private developement repository to have only one public repo.

abn 3.0.5

2024-01-18 Matteo Delucchi

  • Parallelization of buildScoreCache(method='bayes') and fitAbn(method='bayes') with foreach().
  • Controlling the number of cores used by INLA. Before it was always using all available cores.
  • Specifying the type of parallelisation in build.control() and fit.control().
  • Fixed bug in test of simulateAbn() that was failing on CRAN.
  • Increase package availability by skipping tests on CRAN that require INLA. This also speeds up the CRAN checks.

abn 3.0.4

CRAN release: 2023-11-30

2023-11-03 Matteo Delucchi

  • Fixed format issues in source code that caused significant warnings with GCC and clang.
  • Temporary workaround to install the correct versions of INLA dependencies. This will be hopefully fixed in the next release of INLA.

abn 3.0.3

CRAN release: 2023-11-03

2023-11-03 Matteo Delucchi

  • Temporarily fixed tests on CRAN Fedora flavour.

abn 3.0.2

CRAN release: 2023-10-26

2023-10-23 Matteo Delucchi

  • Temporarily fixed tests on CRAN for multithreading.
  • Replaced README.md file.
  • Fixed bug in plotAbn() causing non-sensical edge labels.
  • New CoC and Licence files.
  • Updated examples in documentation.

abn 3.0.1

CRAN release: 2023-10-09

2023-09-29 Matteo Delucchi

  • Patched memory access error in source code.
  • Fixed reverse dependency to mcmcabn().

abn 3.0.0

CRAN release: 2023-09-06

2023-09-01 Matteo Delucchi

  • 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”.

abn 2.7-0

CRAN release: 2022-04-07

2022-04-02 Reinhard Furrer

  • 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.

abn 2.6.0

2021-06-08 Gilles Kratzer, Reinhard Furrer & Kalina Cherneva

  • 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

abn 2.5.0

2021-04-23 Gilles Kratzer & Reinhard Furrer

  • 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

abn 2.4.0

2020-10-31 Gilles Kratzer & Reinhard Furrer

  • Update on citations
  • Update on ORCID number

abn 2.3.0

2020-10-22 Gilles Kratzer & Reinhard Furrer

  • Requirement for use of R>=4.0.0

abn 2.2.1

CRAN release: 2020-06-15

2020-06-13 Gilles Kratzer & Reinhard Furrer

  • Patch for S4 exports not stated in the package
  • Testing automatic (testhat.R in tests repository)
  • Updated version of the vignette

abn 2.2

CRAN release: 2019-11-23

2019-11-22 Gilles Kratzer & Reinhard Furrer

  • 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

abn 2.1

CRAN release: 2019-07-04

2019-07-04 Gilles Kratzer & Reinhard Furrer

  • Compiler flags that were not compatible with the Solaris system
  • Note related to INLA

abn 2.0

CRAN release: 2019-07-01

2019-07-01 Gilles Kratzer & Reinhard Furrer

  • 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

abn 1.2

CRAN release: 2018-08-10

2018-07-23 Gilles Kratzer

  • (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()

abn 1.0.2

CRAN release: 2016-11-09

2016-11-09 Gilles Kratzer

  • Default ban and retain matrix
  • Automatic testing procedure of the package

abn 1.0

CRAN release: 2016-01-18

2016-01-11 Pittavino Marta

  • New vignette uploaded.

abn 0.86

CRAN release: 2015-12-28

2015-12-22 Pittavino Marta

  • INLA routine updated, ERROR and NOTE addressed.

abn 0.85

CRAN release: 2014-12-09

2014-12-22 Pittavino Marta

  • Published Version v0.85 on CRAN

abn 0.85

CRAN release: 2014-12-09

2014-12-09 Pittavino Marta

  • cleanup file to delete additional Makevars added

abn 0.85

CRAN release: 2014-12-09

2014-12-08 Pittavino Marta

  • FOSS license –as-cran NOTE addressed, eliminated BuildVignettes NO in the DESCRIPTION file

abn 0.84

2014-12-06 Pittavino Marta

  • v0.84 submitted to CRAN

abn 0.84

2014-12-05 Pittavino Marta

  • dependencies –as-cran NOTE addressed, with .Rprofile
  • graphical issue with Sweave solved

abn 0.84

2014-12-04 Pittavino Marta

  • finished to edit vignette

abn 0.84

2014-11-23/24 Pittavino Marta

  • updating the vignette

abn 0.84

2014-11-03/04 Pittavino Marta

  • issue with Rd2pdf and LaTeX addressed

abn 0.84

2014-10-27 Pittavino Marta

  • installation of local version of abn to text and work with vignette

abn 0.84

2014-10-23 Pittavino Marta

  • confirmation of the change of maintainer

abn 0.84

2014-10-13 Pittavino Marta

  • updated Rclean for file .log and .status
  • check length characters in manual

abn 0.84

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

abn 0.84

2014-10-03 Pittavino Marta

  • alias Rclean extended
  • eliminate old and very old version
  • comment out require(Cairo) line-code

abn 0.84

2014-10-02 Reinhard Furrer

  • Cairo NOTE fixed, moved from Suggests to Depends
  • DESCRIPTION and NAMESPACE update
  • check if last amendments works
  • .gitignore create

abn 0.84

2014-09-29 Pittavino Marta

  • update version
  • rename R function as the one in manual

abn 0.83

CRAN release: 2013-03-07

2014-09-26 Pittavino Marta

  • update DESCRIPTION

abn 0.83

CRAN release: 2013-03-07

2014-09-19 Pittavino Marta

  • update DESCRIPTION
  • update tographviz documentation
  • create ChangeLog file