2012-11-21 * src/Edges.c (RN_SetNodeParents): Fixed problem with 32 bit version related to parentlist getting overwritten during operation. * src/Registration.c (RN_report_errors): Fixed so that this actually respects number of errors. Also, Fixed in calling program to make default number more like 10. 2012-11-19 Russell G. Almond * src/Networks.c (RN_Named_Nets, RN_GetNth_Nets, isNeticaBN): Added a check for corrupted references which will hopefully prevent a similar problem at the node level. * src/Node.c (isNeticaNode, GetNode_RRef): Added a check to the node reference function which will hopefully fix bogus references. 2012-11-18 Russell G. Almond * R/Node.R (NetworkFindNode): Fixed names of return value. * R/Edges.R (AdjoinNetwork): added a fix for when new nodes are renamed. 2012-11-03 Russell G. Almond * R/Node.R (NetworkNodesInSet): Changed return to be a true list rather than a pairlist, as the latter was causing problems. * R/Edges.R (AdjoinNetwork): Moved this function here. (NetworkFootprint): Added this function. * R/Networks.R (AdjoinNetwork): Added this function, in preparation for EMSM test. 2012-10-29 Russell G. Almond * R/Inference.R (JunctionTreeReport, "EliminationOrder<-") (EliminationOrder, NetworkCompiledSize): Created. * src/Inference.c (RN_SizeCompiledNetwork) (RN_GetEliminationOrder, RN_SetEliminationOrder) (RN_JunctionTreeReport, RN_SplitReport): SplitReport is an auxiliary for JunctionTreeReport which splits report into lines. 2012-10-28 Russell G. Almond * src/Inference.c (RN_NextStates, RN_JointProbability): Created. (RN_MostProbableConfig, RN_FindingProbability): Created. * R/Edges.R (MakeCliqueNode, is.CliqueNode, GetClique): Created. * src/Edges.c (RN_MakeCliqueNode): Created patterned after FormCliqueWith from NeticaEx.c * src/Registration.c (RN_Define_Symbols, RN_Free_Symbols): Added new classes and properties for clique nodes. 2012-10-27 Russell G. Almond * R/Node.R (NetworkNodeSetColor): Changed return value to return set color as a hex string. * src/Node.c (RN_NetworkNodeSetColor): Changed return value to return set color as integer. * R/Node.R (NetworkNodeSets, NodeSets, "NodeSets<-") (NetworkNodesInSet, NetworkSetPriority, NetworkNodeSetColor): Created. * src/Node.c (RN_SetNodeSets, RN_NetworkNodesInSet) (RN_NetworkSetPriority, RN_NetworkNodeSetColor) (RN_NetworkNodeGetColor): Created. 2012-10-26 Russell G. Almond * src/Node.c (RN_NetworkNodesSets, RN_ParseNodeString) (RN_GetNodeSets): Added these functions 2012-10-20 Russell G. Almond * R/Edges.R (is.CPF, as.CPF, is.CPA, as.CPA, parseDims) (integerIndex, selectionToConfig, "[.NeticaNode") ("[[.NeticaNode", "[<-.NeticaNode"): node[] redesign. See Extract.NeticaNode.Rd. * src/Edges.c (RN_GetNodeFuncState, RN_SetNodeFuncState) (RN_GetNodeFuncReal, RN_SetNodeFuncReal): Added as part of the node[] redesign. 2012-10-14 Russell G. Almond * R/Edges.R (is.CPF, as.CPF, is.CPA, as.CPA): Reworked in preparation for node[] Redesign. 2012-10-08 Russell G. Almond * R/Edges.R (as.CPF): Added. 2012-10-05 Russell G. Almond * R/Inference.R (EnterNegativeFinding, "NodeFinding<-") (NodeFinding): Fixed problem with 0-based coding instead of 1-based coding, and with real rather than integer value setting. * src/Inference.c (RN_SetNodeLikelihood, RN_GetNodeLikelihood): Added functions. * R/Inference.R (NodeLikelihood, "NodeLikelihood<-"): Added functions. 2012-10-02 Russell G. Almond * R/Inference.R (CompileNet, UncompileNet, RetractNetFindings) (NodeFinding, "NodeFinding<-", EnterNegativeFinding) (IsBeliefUpdated, NodeBeliefs): * src/Inference.c (RN_CompileNet, RN_UncompileNet) (RN_RetractNetFindings, RN_GetNodeFinding) (RN_RetractNodeFinding, RN_SetNodeFinding, RN_SetNodeFindingNot) (RN_IsBeliefUpdated, RN_GetNodeBeliefs): Wrote these functions * R/Edges.R (DeleteNodeTable, HasNodeTable, IsNodeDeterministic): Added. Preliminary test complete. Note cannot currently set incomplete table. 2012-10-01 Russell G. Almond * src/Edges.c (RN_IsNodeDeterministic, RN_HasNodeTable) (RN_DeleteNodeTable): Addes these table information functions. * R/Edges.R (pStates): Added this function for faster conversions. (nextconfig): Changed to use -1 as the start (as 0 is a legal value with just one parent). (normCPT): Added this function, as we often need it. (parseDims): Started this. Figured out the substitute(list(...)) trick which captures unparsed argument list. * src/Edges.c (RN_AS_PROB_BN, RN_AS_PROBSXP): Modified to convert NAs to UNDEFINED_DBL and vise versa. 2012-09-26 Russell G. Almond * src/Edges.c (RN_SetNodeInputNames, RN_GetNodeInputNames) (RN_GetRelatedNodes, RN_InNodeRelated, RN_AbsorbNodes) (RN_SetNodeParents): Added. * src/Node.c (RN_Copy_Nodes): Fixed issue with AS_NODELIST, note untested. * src/Edges.c (RN_AddLink, RN_DeleteLink, RN_GetNodeParents) (RN_GetNodeChildren): Added * src/Node.c (RN_AS_NODELIST): Changed so that will still NULL in the NODELIST for locations corresponding to NULLs in the R list. 2012-09-25 Russell G. Almond * R/Node.R ("NodeLevels<-", NodeLevels): Created functions. * src/Node.c (RN_GetNodeLevelsDiscrete) (RN_GetNodeLevelsContinuous, RN_SetNodeLevels): Added linking code. Separate getter methods because one returns named object the other does not. * src/Registration.c (RN_RnumToNnum, RN_NnumToRnum): Added conversion functions to take care of converting infinities. 2012-09-24 Russell G. Almond * R/Node.R (NodeNumStates, NodeStates, NodeStates<-) (NodeStateTitles, NodeStateTitles<-, NodeStateDescriptions) (NodeStateDescriptions<-): Added but not tested. 2012-09-23 Russell G. Almond * src/Registration.c (RN_Define_Symbols, RN_Free_Symbols): Added NodeKinds, and XYnames vectors. * R/Node.R (NodeKind, NodeKind<-, NodeVisStyle, NodeVisStyle<-) (NodeVisPos, NodeVisPos): Added and tested. 2012-09-22 Russell G. Almond * R/Networks.R (ReadNetworks, WriteNetworks): Changed these functions so that they tag the return object with the filename. Thus, net <- ReadNetworks(net) should restore a network after an R session is exited. 2012-09-20 Russell G. Almond * DESCRIPTION (Version): Version 0.1-1 -- First experiments, used string IDs. Version 0.1-2 -- Second experiment, added backpointers for Networks Version 0.1-3 -- Added .onLoad methods, complete Network only. Version 0.1-4 -- Preliminary Node Functions