Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X _ _normed_OCE() (in module gunfolds.utils.graphkit) _normed_undirected_OCE() (in module gunfolds.utils.graphkit) _OCE() (in module gunfolds.utils.graphkit) _undirected_OCE() (in module gunfolds.utils.graphkit) A a2edgetuple() (in module gunfolds.conversions) AB2intAB() (in module gunfolds.estimation.linear_model) add2edges() (in module gunfolds.solvers.traversal) add2set_() (in module gunfolds.solvers.unknownrate) add2set_loop() (in module gunfolds.solvers.unknownrate) addaAedge() (in module gunfolds.solvers.traversal) addacedge() (in module gunfolds.solvers.traversal) addanedge() (in module gunfolds.solvers.traversal) (in module gunfolds.utils.graphkit) addapath() (in module gunfolds.solvers.traversal) addAring() (in module gunfolds.utils.graphkit) addavedge() (in module gunfolds.solvers.traversal) addaVpath() (in module gunfolds.solvers.traversal) addedges() (in module gunfolds.utils.graphkit) addselfedge() (in module gunfolds.viz.dbn2latex) adjs2graph() (in module gunfolds.conversions) all_undersamples() (in module gunfolds.utils.bfutils) allsloops() (in module gunfolds.solvers.unknownrate) amap() (in module gunfolds.estimation.linear_model) B bconflictor() (in module gunfolds.solvers.unknownrate) bedgelist() (in module gunfolds.utils.graphkit) bg2num() (in module gunfolds.conversions) bidirected_inc() (in module gunfolds.utils.bfutils) bidirected_no_fork() (in module gunfolds.utils.graphkit) bnf2CG() (in module gunfolds.estimation.linear_model) bp_mean_degree_graph() (in module gunfolds.utils.graphkit) bp_pow_degree_graph() (in module gunfolds.utils.graphkit) build_loop_step() (in module gunfolds.solvers.unknownrate) C c2edgepairs() (in module gunfolds.conversions) cacheconflicts() (in module gunfolds.solvers.unknownrate) call_u_conflicts() (in module gunfolds.utils.bfutils) call_u_conflicts2() (in module gunfolds.utils.bfutils) call_u_conflicts_d() (in module gunfolds.utils.bfutils) call_u_equals() (in module gunfolds.utils.bfutils) call_u_equals2() (in module gunfolds.utils.bfutils) call_undersamples() (in module gunfolds.utils.bfutils) cc_all() (in module gunfolds.utils.bfutils) cc_undersamples() (in module gunfolds.utils.bfutils) cdbn_single() (in module gunfolds.viz.dbn2latex) cdbnprint() (in module gunfolds.viz.dbn2latex) cdbnsingle() (in module gunfolds.viz.dbn2latex) cdbnwrap() (in module gunfolds.viz.dbn2latex) cerror() (in module gunfolds.utils.graphkit) check3() (in module gunfolds.solvers.traversal) check_conflict() (in module gunfolds.utils.bfutils) check_conflict_() (in module gunfolds.utils.bfutils) check_equality() (in module gunfolds.utils.bfutils) checkable() (in module gunfolds.solvers.traversal) checkAedge() (in module gunfolds.solvers.traversal) checkApath() (in module gunfolds.solvers.traversal) checkbedges() (in module gunfolds.solvers.traversal) checkcedge() (in module gunfolds.solvers.traversal) checkedge() (in module gunfolds.solvers.traversal) checker() (in module gunfolds.solvers.traversal) checkerDS() (in module gunfolds.solvers.traversal) checkvedge() (in module gunfolds.solvers.traversal) childrenedges() (in module gunfolds.solvers.traversal) chunks() (in module gunfolds.solvers.traversal) circ_position() (in module gunfolds.viz.gtool) clean_leaf_nodes() (in module gunfolds.utils.graphkit) cleanedges() (in module gunfolds.solvers.traversal) cleanVedges() (in module gunfolds.solvers.traversal) clingo() (in module gunfolds.utils.clingo) clingo2num() (in module gunfolds.conversions) clingo_preamble() (in module gunfolds.conversions) clingo_wedge() (in module gunfolds.conversions) cloneBfree() (in module gunfolds.utils.ecj) cloneempty() (in module gunfolds.solvers.traversal) colorcomponents() (in module gunfolds.viz.gtool) compact_call_undersamples() (in module gunfolds.utils.bfutils) compat() (in module gunfolds.utils.bfutils) compatible() (in module gunfolds.utils.bfutils) compatible_at_u() (in module gunfolds.utils.comparison) complement() (in module gunfolds.utils.graphkit) conflictor() (in module gunfolds.solvers.unknownrate) conflictor_set() (in module gunfolds.solvers.unknownrate) conflictors() (in module gunfolds.solvers.unknownrate) conformanceDS() (in module gunfolds.solvers.traversal) confpairs() (in module gunfolds.solvers.unknownrate) D data2AB() (in module gunfolds.estimation.linear_model) data2graph() (in module gunfolds.estimation.linear_model) data2VARgraph() (in module gunfolds.estimation.linear_model) dbnprint() (in module gunfolds.viz.dbn2latex) decide_absences() (in module gunfolds.estimation.linear_model) degree_ring() (in module gunfolds.utils.graphkit) del2edges() (in module gunfolds.solvers.traversal) del_empty() (in module gunfolds.solvers.traversal) del_loop() (in module gunfolds.solvers.unknownrate) delaAedge() (in module gunfolds.solvers.traversal) delacedge() (in module gunfolds.solvers.traversal) delAloop() (in module gunfolds.solvers.unknownrate) delanedge() (in module gunfolds.solvers.traversal) (in module gunfolds.utils.graphkit) delapath() (in module gunfolds.solvers.traversal) delavedge() (in module gunfolds.solvers.traversal) delaVpath() (in module gunfolds.solvers.traversal) deledges() (in module gunfolds.utils.graphkit) dens2edgenum() (in module gunfolds.utils.bfutils) density() (in module gunfolds.utils.graphkit) dfs_topsort() (in module gunfolds.utils.ecj) dict2graph() (in module gunfolds.viz.dbn2latex) dict_format_converter() (in module gunfolds.conversions) digonly() (in module gunfolds.utils.graphkit) dincrement_u() (in module gunfolds.utils.bfutils) directed_inc() (in module gunfolds.utils.bfutils) dpc() (in module gunfolds.estimation.pc) drasl() (in module gunfolds.solvers.clingo_rasl) drasl_command() (in module gunfolds.solvers.clingo_rasl) drasl_jclingo2g() (in module gunfolds.conversions) drate() (in module gunfolds.solvers.clingo_rasl) drawsamplesLG() (in module gunfolds.estimation.linear_model) drawsamplesMA() (in module gunfolds.estimation.linear_model) E e2num() (in module gunfolds.solvers.unknownrate) edge_function_idx() (in module gunfolds.solvers.traversal) edge_increment_ok() (in module gunfolds.solvers.traversal) edgelist() (in module gunfolds.utils.graphkit) edgenum2dens() (in module gunfolds.utils.bfutils) edgepairs2g() (in module gunfolds.conversions) ekey2e() (in module gunfolds.solvers.unknownrate) emacs_vars() (in module gunfolds.viz.dbn2latex) encode_list_sccs() (in module gunfolds.conversions) encode_sccs() (in module gunfolds.conversions) ensure_gcd1() (in module gunfolds.utils.graphkit) ensure_graph_gcd1() (in module gunfolds.utils.graphkit) esig() (in module gunfolds.solvers.traversal) estimateG() (in module gunfolds.estimation.linear_model) estimateSVAR() (in module gunfolds.estimation.linear_model) every_edge_control_points() (in module gunfolds.viz.gtool) F fdr() (in module gunfolds.estimation.pc) fdrCutoff() (in module gunfolds.estimation.pc) fdrQ() (in module gunfolds.estimation.pc) find_nearest_reachable() (in module gunfolds.utils.neighborhoods) foldplot() (in module gunfolds.viz.dbn2latex) forks() (in module gunfolds.solvers.traversal) forms_loop() (in module gunfolds.utils.bfutils) forward_loop_match() (in module gunfolds.solvers.unknownrate) fullyconnected() (in module gunfolds.utils.graphkit) G G2AH() (in module gunfolds.estimation.linear_model) g2clingo() (in module gunfolds.conversions) g2clingo_msl() (in module gunfolds.solvers.clingo_msl) g2gt() (in module gunfolds.viz.gtool) g2ian() (in module gunfolds.conversions) g2ig() (in module gunfolds.conversions) g2num() (in module gunfolds.conversions) G2SVAR() (in module gunfolds.estimation.linear_model) g2vec() (in module gunfolds.conversions) g2wclingo() (in module gunfolds.conversions) g_single() (in module gunfolds.viz.dbn2latex) gc() (in module gunfolds.estimation.grangercausality) gcd() (in module gunfolds.utils.ecj) gcd1_bp_mean_degree_graph() (in module gunfolds.utils.graphkit) gcd4scc() (in module gunfolds.utils.comparison) (in module gunfolds.utils.graphkit) gen_loops() (in module gunfolds.solvers.unknownrate) genData() (in module gunfolds.estimation.linear_model) get_process_count() (in module gunfolds.utils.calc_procs) getAgraph() (in module gunfolds.estimation.linear_model) getangle() (in module gunfolds.viz.dbn2latex) getAring() (in module gunfolds.estimation.linear_model) getscreensize() (in module gunfolds.viz.gtool) Glag2CG() (in module gunfolds.conversions) glist2str() (in module gunfolds.solvers.clingo_rasl) gmatrix_fold() (in module gunfolds.viz.dbn2latex) gmatrix_list() (in module gunfolds.viz.dbn2latex) gprint() (in module gunfolds.viz.dbn2latex) gpurgepath() (in module gunfolds.solvers.traversal) graph2adj() (in module gunfolds.conversions) graph2badj() (in module gunfolds.conversions) graph2dict() (in module gunfolds.viz.dbn2latex) graph2dot() (in module gunfolds.conversions) graph2nx() (in module gunfolds.conversions) gsig() (in module gunfolds.solvers.traversal) gsingle() (in module gunfolds.viz.dbn2latex) gt2g() (in module gunfolds.viz.gtool) gtranspose() (in module gunfolds.utils.graphkit) H hamming_neighbors() (in module gunfolds.utils.neighborhoods) has_root() (in module gunfolds.utils.comparison) has_self_loops() (in module gunfolds.utils.comparison) has_sink() (in module gunfolds.utils.comparison) has_unit_cycle() (in module gunfolds.utils.ecj) hshift() (in module gunfolds.viz.gtool) I iall() (in module gunfolds.utils.bfutils) ian2g() (in module gunfolds.conversions) icompat() (in module gunfolds.utils.bfutils) ilength() (in module gunfolds.utils.bfutils) inbedgelist() (in module gunfolds.utils.graphkit) increment() (in module gunfolds.utils.bfutils) increment_u() (in module gunfolds.utils.bfutils) independent() (in module gunfolds.estimation.pc) independent_() (in module gunfolds.estimation.pc) inedgelist() (in module gunfolds.utils.graphkit) initRandomMatrix() (in module gunfolds.estimation.linear_model) inorder_check2() (in module gunfolds.solvers.traversal) inorder_checks() (in module gunfolds.solvers.traversal) invertCDSelement() (in module gunfolds.solvers.traversal) is_sclique() (in module gunfolds.utils.bfutils) isAedge() (in module gunfolds.solvers.traversal) isApath() (in module gunfolds.solvers.traversal) isCedge() (in module gunfolds.solvers.traversal) isdedgesubset() (in module gunfolds.utils.graphkit) isedge() (in module gunfolds.solvers.traversal) isedgesubset() (in module gunfolds.utils.graphkit) isvedge() (in module gunfolds.solvers.traversal) iteqclass() (in module gunfolds.solvers.unknownrate) K kernel() (in module gunfolds.estimation.pc) L lconflictors() (in module gunfolds.solvers.unknownrate) lconfpairs() (in module gunfolds.solvers.unknownrate) le2num() (in module gunfolds.solvers.unknownrate) length_d_loopy_paths() (in module gunfolds.solvers.traversal) length_d_paths() (in module gunfolds.solvers.traversal) linegraph() (in module gunfolds.viz.gtool) listgcd() (in module gunfolds.utils.ecj) listgcd_r() (in module gunfolds.utils.ecj) listplace() (in module gunfolds.estimation.linear_model) liteqclass() (in module gunfolds.solvers.unknownrate) load() (in module gunfolds.utils.zickle) loadgraphs() (in module gunfolds.utils.bfutils) longpaths_pick() (in module gunfolds.solvers.traversal) loop2graph() (in module gunfolds.solvers.unknownrate) M main() (in module gunfolds.solvers.unknownrate) make_allforks_and_rest() (in module gunfolds.solvers.traversal) make_emptyforks() (in module gunfolds.solvers.traversal) make_fullforks() (in module gunfolds.solvers.traversal) make_longpaths() (in module gunfolds.solvers.traversal) make_rect() (in module gunfolds.utils.bfutils) makechains() (in module gunfolds.solvers.traversal) makesink() (in module gunfolds.solvers.traversal) makesinks() (in module gunfolds.solvers.traversal) mask2edges() (in module gunfolds.solvers.traversal) maskaAedge() (in module gunfolds.solvers.traversal) maskaCedge() (in module gunfolds.solvers.traversal) maskanedge() (in module gunfolds.solvers.traversal) maskapath() (in module gunfolds.solvers.traversal) maskavedge() (in module gunfolds.solvers.traversal) maskaVpath() (in module gunfolds.solvers.traversal) matchAloop() (in module gunfolds.solvers.unknownrate) matrix_edges() (in module gunfolds.viz.dbn2latex) matrix_end() (in module gunfolds.viz.dbn2latex) matrix_fold() (in module gunfolds.viz.dbn2latex) matrix_grid() (in module gunfolds.viz.dbn2latex) matrix_list() (in module gunfolds.viz.dbn2latex) matrix_start() (in module gunfolds.viz.dbn2latex) mean_degree_graph() (in module gunfolds.utils.graphkit) memo_no_return() (in module gunfolds.solvers.traversal) merge_graphs() (in module gunfolds.utils.graphkit) merge_list() (in module gunfolds.utils.graphkit) moment22() (in module gunfolds.estimation.pc) msl() (in module gunfolds.solvers.clingo_msl) msl_command() (in module gunfolds.solvers.clingo_msl) msl_jclingo2g() (in module gunfolds.conversions) N ncr() (in module gunfolds.utils.neighborhoods) nllf() (in module gunfolds.estimation.linear_model) nllf2() (in module gunfolds.estimation.linear_model) no_children() (in module gunfolds.utils.graphkit) no_parents() (in module gunfolds.utils.graphkit) nodenum() (in module gunfolds.conversions) noiseData() (in module gunfolds.estimation.linear_model) np_fisherZ() (in module gunfolds.estimation.pc) npG2SVAR() (in module gunfolds.estimation.linear_model) num2CG() (in module gunfolds.conversions) num_nATstep() (in module gunfolds.utils.neighborhoods) num_neighbors() (in module gunfolds.utils.neighborhoods) numbered_g2clingo() (in module gunfolds.conversions) numbered_g2wclingo() (in module gunfolds.conversions) nx2graph() (in module gunfolds.conversions) nxbp2graph() (in module gunfolds.conversions) O OCE() (in module gunfolds.utils.graphkit) oerror() (in module gunfolds.utils.graphkit) ok2add2edges() (in module gunfolds.solvers.traversal) ok2addaAedge() (in module gunfolds.solvers.traversal) ok2addacedge() (in module gunfolds.solvers.traversal) ok2addanedge() (in module gunfolds.solvers.traversal) ok2addanedge1() (in module gunfolds.solvers.traversal) ok2addanedge2() (in module gunfolds.solvers.traversal) ok2addapath() (in module gunfolds.solvers.traversal) ok2addavedge() (in module gunfolds.solvers.traversal) ok2addaVpath() (in module gunfolds.solvers.traversal) old_g2clingo() (in module gunfolds.conversions) output_graph_figure() (in module gunfolds.viz.dbn2latex) overshoot() (in module gunfolds.utils.bfutils) P paintSCC() (in module gunfolds.viz.dbn2latex) perm_circular() (in module gunfolds.solvers.unknownrate) plotg() (in module gunfolds.viz.gtool) plotgunfolds() (in module gunfolds.viz.gtool) pow_degree_graph() (in module gunfolds.utils.graphkit) presence_probs() (in module gunfolds.estimation.linear_model) print_loops() (in module gunfolds.utils.simpleloops) prune_conflicts() (in module gunfolds.solvers.unknownrate) prune_loops() (in module gunfolds.solvers.unknownrate) prune_sort_CDS() (in module gunfolds.solvers.traversal) prunepaths_1D() (in module gunfolds.solvers.traversal) pure_directed_inc() (in module gunfolds.utils.bfutils) purgepath() (in module gunfolds.solvers.traversal) R randH() (in module gunfolds.utils.graphkit) randomDAG() (in module gunfolds.utils.graphkit) randomSVAR() (in module gunfolds.estimation.linear_model) randomSVARs() (in module gunfolds.estimation.linear_model) randomTRIL() (in module gunfolds.utils.graphkit) randSCC() (in module gunfolds.utils.comparison) randweights() (in module gunfolds.estimation.linear_model) rasl() (in module gunfolds.solvers.clingo_rasl) rasl_a2edgetuple() (in module gunfolds.conversions) rasl_c2edgepairs() (in module gunfolds.conversions) rasl_command() (in module gunfolds.solvers.clingo_rasl) rasl_jclingo2g() (in module gunfolds.conversions) rasl_msl() (in module gunfolds.solvers.clingo_msl) rate() (in module gunfolds.conversions) (in module gunfolds.solvers.clingo_msl) (in module gunfolds.solvers.clingo_rasl) reachable() (in module gunfolds.utils.ecj) remove_loop() (in module gunfolds.utils.graphkit) remove_tril_singletons() (in module gunfolds.utils.graphkit) residuals_() (in module gunfolds.estimation.pc) reverse() (in module gunfolds.solvers.unknownrate) reverse_edge_match() (in module gunfolds.solvers.unknownrate) reverse_loop_match() (in module gunfolds.solvers.unknownrate) ring() (in module gunfolds.utils.graphkit) ring_sccs() (in module gunfolds.utils.graphkit) ringarcs() (in module gunfolds.utils.graphkit) ringmore() (in module gunfolds.utils.graphkit) run_clingo() (in module gunfolds.utils.clingo) S sampleWeights() (in module gunfolds.estimation.linear_model) save() (in module gunfolds.utils.zickle) savegraphs() (in module gunfolds.utils.bfutils) scale_free() (in module gunfolds.utils.graphkit) scc() (in module gunfolds.utils.ecj) scc_unreachable() (in module gunfolds.utils.graphkit) scoreAGraph() (in module gunfolds.estimation.linear_model) search_match() (in module gunfolds.utils.comparison) selfloop() (in module gunfolds.utils.graphkit) selfloops() (in module gunfolds.solvers.traversal) shift_labels() (in module gunfolds.utils.graphkit) shift_list_labels() (in module gunfolds.utils.graphkit) signature() (in module gunfolds.solvers.traversal) simple_loops() (in module gunfolds.utils.simpleloops) single_nodes() (in module gunfolds.solvers.traversal) skip_conflict() (in module gunfolds.solvers.unknownrate) skip_conflictors() (in module gunfolds.solvers.unknownrate) SM_converging() (in module gunfolds.utils.comparison) SM_fixed() (in module gunfolds.utils.comparison) stableVAR() (in module gunfolds.estimation.linear_model) start_progress_bar() (in module gunfolds.solvers.unknownrate) subgraph() (in module gunfolds.utils.graphkit) superclique() (in module gunfolds.utils.graphkit) supergraphs_in_eq() (in module gunfolds.solvers.traversal) symchol() (in module gunfolds.estimation.linear_model) T threedges_pick() (in module gunfolds.solvers.traversal) timeout() (in module gunfolds.utils.myTimeout) tr() (in module gunfolds.utils.ecj) transitionMatrix() (in module gunfolds.estimation.linear_model) transitionMatrix2() (in module gunfolds.estimation.linear_model) transitionMatrix3() (in module gunfolds.estimation.linear_model) transitionMatrix4() (in module gunfolds.estimation.linear_model) try_till_d_path() (in module gunfolds.solvers.traversal) try_till_path() (in module gunfolds.solvers.traversal) twoedges_pick() (in module gunfolds.solvers.traversal) U udensity() (in module gunfolds.utils.graphkit) ug2num() (in module gunfolds.conversions) undedgelist() (in module gunfolds.utils.graphkit) undersample() (in module gunfolds.utils.bfutils) unfoldplot() (in module gunfolds.viz.dbn2latex) upairs() (in module gunfolds.utils.graphkit) update_graph() (in module gunfolds.utils.graphkit) V v2g22g1() (in module gunfolds.solvers.traversal) VARbic() (in module gunfolds.estimation.linear_model) vec2adj() (in module gunfolds.conversions) vec2g() (in module gunfolds.conversions) vedgelist() (in module gunfolds.solvers.traversal) W walk() (in module gunfolds.utils.ecj) weight_and_mask() (in module gunfolds.estimation.linear_model) weighted_drasl_program() (in module gunfolds.solvers.clingo_rasl) X x2M() (in module gunfolds.estimation.linear_model)