NAMESPACE_old

useDynLib(IMaGES, .registration = TRUE)

###----- Imports ------------------------------------------------------

importFrom("stats", cor, cor.test, cov, cov2cor,
           fisher.test, pchisq, pnorm, qnorm,
           rbinom, rcauchy, rnorm, rt, runif,
           sd, setNames, symnum, uniroot)

importFrom("utils", combn, str)

importFrom("graphics", par, plot.default, plot, title)

importMethodsFrom("methods", coerce, show)
importFrom("methods",
           setClass, setClassUnion, setMethod, setOldClass, setValidity,
           getClass, getClassDef, callGeneric, as, is, extends,
	   new, validObject,
	   signature, representation, prototype)

## aargh: slow loading {currently just for getGraph() and similar}
## importFrom("Matrix", coerce)
## importClassesFrom("Matrix", Matrix, sparseMatrix, TsparseMatrix)

importFrom("abind", abind)
importFrom("corpcor", pseudoinverse)

importFrom("robustbase",
	   covOGK, hard.rejection,
	   Qn, s_Qn, scaleTau2 #, Sn, s_Sn, s_mad, s_IQR
	   )

importFrom("graph",
           edgeNames, reverseEdgeDirections,
           edgeRenderInfo, nodes, "edgeRenderInfo<-")
importClassesFrom("graph", graph, graphAM, graphNEL)
importMethodsFrom("graph",
		  ## addEdge,
		  coerce,# as(., ...)
		  edges, edgeData,
		  edgeDataDefaults, "edgeDataDefaults<-",
		  isDirected,
		  nodes, "nodes<-",
		  numNodes, numEdges,
		  subGraph, ugraph)

importFrom("igraph", graph.adjacency, igraph.from.graphNEL, is.chordal,
	   plot.igraph, graph.dfs, k.regular.game, get.adjacency, get.edgelist,
           watts.strogatz.game, simplify, bipartite.random.game,
           barabasi.game, interconnected.islands.game, degree.sequence.game)

importFrom("RBGL",
	   biConnComp, johnson.all.pairs.sp, separates, bfs, connectedComp)
## also    sp.between -- but only for deprecated beta.special(), hence RBGL::*

importFrom("ggm", isAcyclic, transClos, topOrder, msep)
importFrom("Rcpp", evalCpp) # Needed for any package relying on Rcpp headers...
  # Otherwise, there are runtime errors.

importFrom("bdsmatrix", gchol) ## for jointIda ("MCD")

importFrom("sfsmisc", digitsBase, is.whole)

importFrom("fastICA", fastICA)
importFrom("clue", solve_LSAP)
importFrom("gmp", as.bigz, chooseZ, as.bigq)
importFrom("dagitty", dagitty, isAdjustmentSet, adjustmentSets)

importFrom("lavaan", sem, partable)

importFrom("Rgraphviz", agopen)

###----- Exports ------------------------------------------------------

#export(getGraph)# our S4 generic including methods

#export(trueCov,
#       randomDAG,
#       wgtMatrix,
#       rmvDAG,
#       pcSelect,
#       zStat,
#       condIndFisherZ,
#       pcorOrder,
#       compareGraphs,
#       getNextSet,
#       mcor,
#       pcSelect.presel,
#       corGraph,
#       dag2cpdag,
#       ## adj.check,
#       udag2pdag, udag2pdagSpecial, udag2pdagRelaxed,
#       shd,
#       pcAlgo, pcAlgo.Perfect,
#       pdag2dag,
#       udag2pag,
#       beta.special,
#       beta.special.pcObj,
#       causalEffect,
#       dreach, qreach,
#       plotAG,
#       skeleton,
#       pc,
#       gSquareBin,
#       gSquareDis,
#       gaussCItest,
#       # gaussCItest.fast,
#       dsep,
#       dsepTest,
#       disCItest,
#       binCItest,
#       ida,
#       idaFast,
#       legal.path,
#       plotSG,
#       pc.cons.intern,
#       checkTriple,
#       triple2numb,
#       fci,
#       pdsep,
#       rfci,
#       find.unsh.triple,
#       udag2apag,
#       dag2pag, # skeleton.dag2pag,
#       iplotPC,
#       showEdgeList,
#       showAmat,
#       visibleEdge,
#       possibleDe,
#       pag2magAM,
#       backdoor,
#       jointIda,
#       ## Alain's :
#       r.gauss.pardag,
#       rmvnorm.ivent,
#       gies,
#       ges,
#       gds,
#       simy,
#       mat2targets,
#       targets2mat,
#       dag2essgraph,
#       ## --- end{Alain}
#       fciPlus,
#       lingam, LINGAM,
#      randDAG,
#       unifDAG,
#       unifDAG.approx,
#       gac,
#      ## no longer: use as(*,"amat")
#       ##  displayAmat,
#       pdag2allDags,
#       possDe,
#       possAn,
#       pcalg2dagitty,
#       addBgKnowledge,
#       adjustment,
#       isValidGraph,
#       IMaGES,
#       plotIMGraph,
#       plotAll,
#       plotMarkovs)

export(IMaGES,
       plotIMGraph,
       plotAll,
       plotMarkovs)

## These are "internal" i.e., in man/pcalg-internal.Rd
## _FIXME ?_                     ---------------------
#export(##ancTS,
       ## has.new.coll,
       ## ci.test,
       ## dep.triple,
       ## faith.check,
       ## find.sink,
       ## flipEdges,
       ## minUncovCircPath,
       ## minUncovPdPath,
       ## minDiscrPath,
       ## my.SpecialDag,
       ## reach, # NB: dreach(), qreach() *are* non-internal
       ## updateList,
       ## FIXME{MM}: document !
#       rfci.vStruc,
#       allDags,
#       amat2dag)


exportClasses(#"pcAlgo",
#              "fciAlgo",
#              "gAlgo",
#              "ParDAG",
#              "GaussParDAG",
#              "Score",
#              "GaussL0penIntScore",
#              "GaussL0penObsScore",
#              "EssGraph",
              "IMaGES",
              "IMGraph")

#exportMethods(# needed? "coerce",# <- defined via setAs(., ..) used via  as(A, "class_B")
#              "summary", "show", "plot")

#S3method(print, fciAlgo)
#S3method(print, pcAlgo)
#S3method(print, amat)
## FIXME: TODO
# S3method(print, LINGAM)