2020-01-14 Søren Højsgaard * Minor flaws fixed * Version 1.8-5.2 uploaded 2020-01-07 Søren Højsgaard * 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 * Minor updates * All exports are made explicit * Version 1.8-4.5 uploaded 2018-12-12 Søren Højsgaard * random_dag changed so that maxpar parents can be obtained; before it was maxpar-1 * glist2setMAT reintrouced 2018-07-12 Søren Højsgaard * Minor changes, including fixing a warning from CRAN * Cleaning of array operations * Version 1.8-4 uploaded 2017-03-20 Søren Højsgaard * 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 * 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 * 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 * Fixed quotes in DESRIPTION file * Version 1.7-5 uploaded. 2016-02-14 Søren Højsgaard * Fixed issue about isinf in cpp files * Version 1.7-4 uploaded. 2015-12-31 Søren Højsgaard * 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 * 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 * 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 * 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 * 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 * Bug in rip() function fixed. Thanks to Vanessa Didelez for the bug report. * Version 1.6-12 uploaded. 2013-06-25 Søren Højsgaard * 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 * 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 * simulateArray and glist2setMAT from gRain moved to gRbase * minor cleanups * Version 1.6-8 uploaded. 2013-01-29 Søren Højsgaard * 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 * 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 * 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 * 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 * 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 * Change of Makevars file to pass checks on linux * Version 1.6-2 uploaded 2012-08-04 Søren Højsgaard * Smaller changes to documentation, including proper markup of email adresses. * Version 1.6-1 uploaded 2012-07-27 Søren Højsgaard * 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 * Dependency on igraph changed to igraph0 * Version 1.5-1 uploaded 2012-02-28 Søren Højsgaard * Update of URL, version number and CITATION file * Version 1.5-0 uploaded 2012-01-17 Søren Højsgaard * Small changes to package structure * Version 1.4.4 uploaded 2012-01-17 Søren Højsgaard * URL updated * Version 1.4.3 uploaded 2011-12-30 Søren Højsgaard * Plot method for junction tree (rip ordering) added. * E-mail address changed * Version 1.4.2 uploaded 2011-09-07 Søren Højsgaard * Smaller issue regarding charmatch vs match * Version 1.4.1 uploaded 2011-07-20 Søren Højsgaard * 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 * Minor fixes * Version 1.3.9 uploaded 2011-01-07 Søren Højsgaard * Fixes in vignettes * BodyFat data added * Version 1.3.8 uploaded 2011-01-07 Søren Højsgaard * All calls to .Internal have been removed * Version 1.3.7 uploaded 2011-01-07 Søren Højsgaard * C-code has been reorganized * Vignettes have been added. * Version 1.3.6 uploaded 2010-12-20 Søren Højsgaard * Generic iplot function added * Version 1.3.5 uploaded 2010-02-24 Søren Højsgaard * edgeList and nonEdgeList reimplemented * Version 1.3.4 uploaded 2010-02-17 Søren Højsgaard * Fix of generic triangulate function * Version 1.3.3 uploaded 2010-02-11 Søren Højsgaard * 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 * names2pairs reimplemented * Datasets milkcomp and ashtrees added * version 1.3.1 uploaded 2009-12-29 Søren Højsgaard * 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 * 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 * First argument to fit is now 'object' rather than 'm' * conc2pcor function added. * Version 1.1.3 uploaded 2009-06-28 Søren Højsgaard * 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 * Speedups of various functions; cleaning up some code. * Version 1.1.0 uploaded 2009-02-21 Søren Højsgaard * maxCliqueMAT added * mcsMAT implemented in C * Bug fixed in moralizeMAT * Version 1.0.0 uploaded 2009-02-11 Søren Højsgaard * Vignette about graphs added. * More datasets added. * Version 0.9.0 uploaded 2009-01-22 Søren Højsgaard * 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 * 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 * is.decomposition fixed. 2008-12-17 Søren Højsgaard * newDAG, newUG etc are now removed * edgePairs now removed * Version 0.6.6 uploaded 2008-12-11 Søren Højsgaard * 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 * 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 * 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 * triangulation algorithms from gRain moved to gRbase * Version 0.6.0 uploaded 2008-09-09 Søren Højsgaard * 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 * processFormula extended * Version 0.4.2 uploaded 2008-05-01 Søren Højsgaard * Minor changes for compatability with other gR-related packages * Version 0.4.1 uploaded 2008-04-24 Søren Højsgaard * Minor changes made to match R 2.7.0 * Reorganizing code structure * Version 0.4.0 uploaded 2008-04-15 Søren Højsgaard * 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 * C implementation of certain set operations (remove.redundant, isin). * names2pairs and subsetof included. * Version 0.3.1 uploaded 2008-03-10 Søren Højsgaard * Arguments of generic fit function changed * Version 0.2.6 uploaded. 2008-02-28 Søren Højsgaard * breastcancer data has been corrected * Version 0.2.5 uploaded. 2008-01-07 Søren Højsgaard * Breast cancer data set added. * Reinis data stored as RData object * Version 0.2.4 uploaded. 2007-11-25 Søren Højsgaard * 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 * 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 * Minor typos in the docs corrected * Version 0.2.1 uploaded 2007-10-16 Søren Højsgaard * 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 * 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