2020-01-14 Søren Højsgaard <sorenh@math.aau.dk>

	* Minor flaws fixed

	* Version 1.8-5.2 uploaded
	
2020-01-07 Søren Højsgaard <sorenh@math.aau.dk>

	* Rgraphviz needs no longer be loaded to plot a graph

	* It is handled that in the future, that the class of a matrix is
	also an array.

	* is.DAG renamed to is_dag and similarly for friends. Old versions
	retained for backward compatibility.

	* Mess as been cleaned up

	* Version 1.8-5.1 uploaded

2019-09-25 Søren Højsgaard <sorenh@math.aau.dk>

	* Minor updates

	* All exports are made explicit

	* Version 1.8-4.5 uploaded

2018-12-12 Søren Højsgaard <sorenh@math.aau.dk>

	* random_dag changed so that maxpar parents can be obtained; before it was maxpar-1

	* glist2setMAT reintrouced

2018-07-12 Søren Højsgaard <sorenh@math.aau.dk>

	* Minor changes, including fixing a warning from CRAN

	* Cleaning of array operations

	* Version 1.8-4 uploaded

2017-03-20 Søren Højsgaard <sorenh@math.aau.dk>

	* Version 1.8-2 never made it to CRAN because of an error.

	* All the registration of c-routines done

	* Version 1.8-3 uploaded

2017-02-05 Søren Højsgaard <sorenh@math.aau.dk>

	* Added %a==%, %a/0%, %a_% (tabMarg) %a^% tabExpand

	* arxxx functions renamed to ar_xxx -- may well change in the
	future; not too happy with these names.

	* vchi (v, ch(v)) added

	* Bug in tabDiv0 fixed

	* gRain-array vignette rewritten

	* Misc stuff to facilitate gRain improvements

	* triang methods added to facilitat triang_mcwh and triang_elo
	  (triangulation where an elimination order is given).

	* Class parray removed on arrays

	* Version 1.8-2 uploaded

2016-10-16 Søren Højsgaard <sorenh@math.aau.dk>

	* gRbase rewritten using roxygen
	* New naming conventions for array-operations: The internal
	implementation names are like tabPerm, tabAdd etc. (they are
	visible to the user and are used in eg. gRain). But the names
	intended to be used by users are arperm aradd etc.
	* In binary array operations it is now being checked that the
	dimnames match.
	* Version 1.8-1 uploaded

2016-02-14 Søren Højsgaard <sorenh@math.aau.dk>

	* Fixed quotes in DESRIPTION file
	* Version 1.7-5 uploaded.

2016-02-14 Søren Højsgaard <sorenh@math.aau.dk>

	* Fixed issue about isinf in cpp files
	* Version 1.7-4 uploaded.

2015-12-31 Søren Højsgaard <sorenh@math.aau.dk>

	* moralizeMAT fails if matrix does not have dimnames. Fixed
	now. Thanks to David Edwards for reporting bug.
	* Version 1.7-3 uploaded.

2015-10-10 Søren Højsgaard <sorenh@math.aau.dk>

	* Corrected use of log and fabs in c++ code; thanks to BDR for
	pointing this out
	* get_subset_ added
	* ug2dag added (works only on graphNEL's)
	* Version 1.7-2 uploaded.

2015-08-20 Søren Højsgaard <sorenh@math.aau.dk>

	* is.adjMAT is now based on own c++ code; way faster.
	* get_superset_ and is_subsetof_ added.
	* names2pairsM added.
	* graph conversion utilities reworked.
	* check argument added to triangulate; controls if it is checked
	that a graph is triangulated.
	* New vignettes
	* Version 1.7-1 uploaded.

2014-06-26 Søren Højsgaard <sorenh@math.aau.dk>

	* tableSetSliceValue and tableGetSliceIndex functions added.
	* 'margin' in tableMargin can be a right-hand-sided formula.
	* Version 1.7-0.1 uploaded.

2014-03-17 Søren Højsgaard <sorenh@math.aau.dk>

	* Added array functions (arrayPerm, arrayMargin, arrayOp
	etc). These are implemented using Rcpp, they are not documented
	but illustrated in a vignette.
	* Many new implementations of graph/matrix operations with Rcpp.
	* Major cleanups
	* Version 1.7-0 uploaded.

2013-07-17 Søren Højsgaard <sorenh@math.aau.dk>

	* Bug in rip() function fixed. Thanks to Vanessa Didelez for the
	bug report.
	* Version 1.6-12 uploaded.

2013-06-25 Søren Højsgaard <sorenh@math.aau.dk>

	* Changes in NAMESPACE file such that the entire RBGL package is
	not loaded.
	* Makefile added for building vignettes
	* Version 1.6-10 uploaded.

2013-05-28 Søren Højsgaard <sorenh@math.aau.dk>

	* The use of fmatch has been replaced by the use of mathc.
	* ripMAT re-implemented; much faster.
	* Version 1.6-9 uploaded.

2013-03-10 Søren Højsgaard <sorenh@math.aau.dk>

	* simulateArray and glist2setMAT from gRain moved to gRbase
	* minor cleanups
	* Version 1.6-8 uploaded.

2013-01-29 Søren Højsgaard <sorenh@math.aau.dk>

	* mcsMAT now implemented via Rcpp for sparse (dgCMatrix)
	and dense matrices.

	* ripMAT re-implemented in R. Much faster now, but a C
	implementation is on the todo-list.

	* bug fixed in asdgCMatrix.

	* getCliques implemented.

	* Vignettes are improved.

	* Version 1.6-7 uploaded.

2013-01-08 Søren Højsgaard <sorenh@math.aau.dk>

	* triangulateMAT now implemented via Rcpp for sparse (dgCMatrix)
	and dense matrices.

	* asdgCMatrix function added. Fast coercion from dense to
	dgCMatrix.

	* ripMAT now also returns childList; the children of each node in
	the junction tree.

	* Version 1.6-6 uploaded

2012-12-27 Søren Højsgaard <sorenh@math.aau.dk>

	* is.UG, is.DAG, is.TUG added

	* Support for representing graphs as sparse matrices (dgCMatrix matrices from the
	Matrix package).

	* solveSPD for finding the inverse of symmetric positive definite
	matrix added.

	* random_dag function added

	* Version 1.6-5 uploaded

2012-10-07 Søren Højsgaard <sorenh@math.aau.dk>

	* Minor changes to the DESCRIPTION file

	* Change of maxCliqueMAT (made possible be a change in RBGL;
	thanks to Vincent Carey.

	* Version 1.6-4 uploaded

2012-09-25 Søren Højsgaard <sorenh@math.aau.dk>

	* Bug in C code for mcs (maximum cardinality search)
	detected. Problem solved be using R version of mcs.

	* mcsmarkedMAT speeded up

	* update of DESCRIPTION file

	* Version 1.6-3 uploaded

2012-08-05 Søren Højsgaard <sorenh@math.aau.dk>

	* Change of Makevars file to pass checks on linux

	* Version 1.6-2 uploaded

2012-08-04 Søren Højsgaard <sorenh@math.aau.dk>

	* Smaller changes to documentation, including proper markup of
	email adresses.

	* Version 1.6-1 uploaded

2012-07-27 Søren Højsgaard <sorenh@math.aau.dk>

	* Package changed such that it depends on igraph now (and not the
	more obsolete igraph0 package)

	* Facilities for working with graphs represented as sparse
	matrices have been added.

	* Version 1.6-0 uploaded

2012-06-13 Søren Højsgaard <sorenh@math.aau.dk>

	* Dependency on igraph changed to igraph0

	* Version 1.5-1 uploaded

2012-02-28 Søren Højsgaard <sorenh@math.aau.dk>

	* Update of URL, version number and CITATION file

	* Version 1.5-0 uploaded

2012-01-17 Søren Højsgaard <sorenh@math.aau.dk>

	* Small changes to package structure

	* Version 1.4.4 uploaded

2012-01-17 Søren Højsgaard <sorenh@math.aau.dk>

	* URL updated

	* Version 1.4.3 uploaded

2011-12-30 Søren Højsgaard <sorenh@agrsci.dk>

	* Plot method for junction tree (rip ordering) added.

	* E-mail address changed

	* Version 1.4.2 uploaded

2011-09-07 Søren Højsgaard <sorenh@agrsci.dk>

	* Smaller issue regarding charmatch vs match

	* Version 1.4.1 uploaded

2011-07-20 Søren Højsgaard <sorenh@agrsci.dk>

	* as methods for graph coercion added

	* Minor speedups

	* rowmat2list and colmat2list added.

	* Methods added for the slightly more advanced graph algorithms.

	* Datasets dumping, wine and Nutrimouse added.

	* Version 1.4.0 uploaded


2011-01-11 Søren Højsgaard <sorenh@agrsci.dk>

	* Minor fixes

	* Version 1.3.9 uploaded

2011-01-07 Søren Højsgaard <sorenh@agrsci.dk>

	* Fixes in vignettes

	* BodyFat data added

	* Version 1.3.8 uploaded

2011-01-07 Søren Højsgaard <sorenh@agrsci.dk>

	* All calls to .Internal have been removed

	* Version 1.3.7 uploaded

2011-01-07 Søren Højsgaard <sorenh@agrsci.dk>

	* C-code has been reorganized

	* Vignettes have been added.

	* Version 1.3.6 uploaded

2010-12-20 Søren Højsgaard <sorenh@agrsci.dk>

	* Generic iplot function added

	* Version 1.3.5 uploaded

2010-02-24 Søren Højsgaard <sorenh@agrsci.dk>

	* edgeList and nonEdgeList reimplemented

	* Version 1.3.4 uploaded

2010-02-17 Søren Højsgaard <sorenh@agrsci.dk>

	* Fix of generic triangulate function

	* Version 1.3.3 uploaded

2010-02-11 Søren Højsgaard <sorenh@agrsci.dk>

	* triangulate has been made gereric and a triangulate.graphNEL
	function has been added.

	* Functions propagate and compile have been made generic

	* Version 1.3.2 uploaded

2010-01-10 Søren Højsgaard <sorenh@agrsci.dk>

	* names2pairs reimplemented

	* Datasets milkcomp and ashtrees added

	* version 1.3.1 uploaded


2009-12-29 Søren Højsgaard <sorenh@agrsci.dk>

	* Function combnPrim (a C version of combn) for finding all m
	combinations of n elements has been added.

	* Version 1.3.0 uploaded

2009-12-27 Søren Højsgaard <sorenh@agrsci.dk>

	* Functions for finding a minimal triangulation of undirected
	graph ('minimalTriang' and 'minimalTriangMAT') added. Code kindly
	provided by Clive Bowsher.

	* Functions for finding maximal prime subgraph decomposition of
	undirected graph ('mpd' and 'mpdMAT') added. Code kindly
	provided by Clive Bowsher.

	* Version 1.2.0 uploaded

2009-06-28 Søren Højsgaard <sorenh@agrsci.dk>

	* First argument to fit is now 'object' rather than 'm'

	* conc2pcor function added.

	* Version 1.1.3 uploaded

2009-06-28 Søren Højsgaard <sorenh@agrsci.dk>

	* rip failed when a graph had only one node. Fixed now.

	* triangmcwh failed on 64 bit machines due to a memory leak. Fix
	provided by Charles Brundell. Thanks.

	* Version 1.1.2 uploaded

2009-04-26 Søren Højsgaard <sorenh@agrsci.dk>

	* Speedups of various functions; cleaning up some code.

	* Version 1.1.0 uploaded

2009-02-21 Søren Højsgaard <sorenh@agrsci.dk>

	* maxCliqueMAT added

	* mcsMAT implemented in C

	* Bug fixed in moralizeMAT

	* Version 1.0.0 uploaded


2009-02-11 Søren Højsgaard <sorenh@agrsci.dk>

	* Vignette about graphs added.

	* More datasets added.

	* Version 0.9.0 uploaded


2009-01-22 Søren Højsgaard <sorenh@agrsci.dk>

	* Bug fixed in rhsFormula2list

	* Calls to aperm replaced with .Internal(aperm...) whenever
	possible (for speed)

	* Miscellaneous other speed ups.

	* Various xxxMAT functions added for graph algorithms on adjancecy matrices

	* Version 0.8.0 uploaded

2009-01-05 Søren Højsgaard <sorenh@agrsci.dk>

	* Bug fixed in MCS (failed if graph was not chordal)

	* add.edge and delete.edge renamed to .add.edge and .delete.edge
	to avoid conflicts with RHugin

	* Version 0.7.0 uploaded


2008-12-17 Søren Højsgaard <sorenh@agrsci.dk>

	* is.decomposition fixed.



2008-12-17 Søren Højsgaard <sorenh@agrsci.dk>

	* newDAG, newUG etc are now removed

	* edgePairs now removed

	* Version 0.6.6 uploaded


2008-12-11 Søren Højsgaard <sorenh@agrsci.dk>

	* cov2pcor function added.

	* MCS function fixed to return indices correctly when 'root'
	argument is used.

	* Version 0.6.5 uploaded

2008-12-04 Søren Højsgaard <sorenh@agrsci.dk>

	* MCS now returns character(0) when MCS fails

	* RIP now returns list() when RIP fails.

	* Version 0.6.4 uploaded

2008-11-05 Søren Højsgaard <sorenh@agrsci.dk>

	* Functions ug(), dag(), ugList() and dagList() now replace
	newUG(), newDAG(), newUGlist() and newDAGlist()

	* A collection of graph operations have been added

	* carcassall data have been added

	* edgeList and nonEdgeList functions added

	* pairs2num function added


2008-10-13 Søren Højsgaard <sorenh@agrsci.dk>

	* triangulation algorithms from gRain moved to gRbase

	* Version 0.6.0 uploaded

2008-09-09 Søren Højsgaard <sorenh@agrsci.dk>

	* General table operations functions added (taken from gRain)

	* Functions for specifying graphs in graphNEL format added (newUG
	and newDAG)

	* MCS, RIP and querygraph functions added.

	* Version 0.5.0 uploaded


2008-07-12 Søren Højsgaard <sorenh@agrsci.dk>

	* processFormula extended

	* Version 0.4.2 uploaded

2008-05-01 Søren Højsgaard <sorenh@agrsci.dk>

	* Minor changes for compatability with other gR-related packages

	* Version 0.4.1 uploaded


2008-04-24 Søren Højsgaard <sorenh@agrsci.dk>

	* Minor changes made to match R 2.7.0

	* Reorganizing code structure

	* Version 0.4.0 uploaded


2008-04-15 Søren Højsgaard <sorenh@agrsci.dk>

	* uniquePrim, setdiffPrim, unlistPrim added

	* Speed improved of remove.redundant, isin

	* Speed improved of dual.rep

	* Version 0.3.2 uploaded

2008-03-25 Søren Højsgaard <sorenh@agrsci.dk>

	* C implementation of certain set operations (remove.redundant,
	isin).

	* names2pairs and subsetof included.

	* Version 0.3.1 uploaded

2008-03-10 Søren Højsgaard <sorenh@agrsci.dk>

	* Arguments of generic fit function changed

	* Version 0.2.6 uploaded.


2008-02-28 Søren Højsgaard <sorenh@agrsci.dk>

	* breastcancer data has been corrected

	* Version 0.2.5 uploaded.


2008-01-07 Søren Højsgaard <sorenh@agrsci.dk>

	* Breast cancer data set added.

	* Reinis data stored as RData object

	* Version 0.2.4 uploaded.


2007-11-25 Søren Højsgaard <sorenh@agrsci.dk>

	* Functions shortNames, varTypes and nLevels now returns named
	vectors.

	* Bug when nLevels is created automatically is fixed.

	* Version 0.2.3 uploaded.


2007-11-07 Søren Højsgaard <sorenh@agrsci.dk>

	* All the info printed on startup has been removed.

	* Coronary artery disease data now properly described. They are in
	data sets cad1 and cad2.

	* Version 0.2.2 uploaded


2007-10-24 Søren Højsgaard <sorenh@agrsci.dk>

	* Minor typos in the docs corrected

	* Version 0.2.1 uploaded

2007-10-16 Søren Højsgaard <sorenh@agrsci.dk>

	* newgmData can infer valueLabels automatically

	* Rewriting of gmData part in vignette

	* addEdge/dropEdge have been removed because they collide with the
	graph package. As an alternative, an update.gModel method added
	(this needs more work).


2007-05-13 Søren Højsgaard <sorenh@agrsci.dk>

	* This change log file has been introduced; please add to it from
	the top

	* description function for gmData is removed (collides with
	generic description function from graph package).

	* newgmData modified: Makes shortNames to be of length 1 if at all
	possible. Sets dataOrigin as the class of the observations.

	* dataOrigin function for gmData added.

	* ordinal, ordinal<-, nominal, nominal functions for gmData
	added.

	* Version number changed to 0.2.0

	* ZipData: no added to description file

	* cad-data: A .R file has been added to read data as factors