A Package for Graphical Modelling in R
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Documentation for package ‘gRbase’ version 2.0.2
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
A B C D E F G I J L M N O P Q R S T U V W misc
-- A --
| addEdge | Query a graph |
| addEdge.gModel | Internal functions for the gRbase package |
| adj | Query a graph |
| all_pairs | Create all possible pairs |
| all_subsets | Create all subsets |
| all_subsets0 | Create all subsets |
| ancestors | Query a graph |
| ancestralGraph | Query a graph |
| ancestralSet | Query a graph |
| api-array-07 | Array operations (2007) |
| api-array-properties | Check if object is array |
| api-cell | Table cell operations. |
| api-cell_ | Low level table cell operations implemented in c++ |
| api-parray | Representation of and operations on multidimensional arrays |
| api-pct-operations | Array algebra |
| api-tabDist | Marginalize and condition in multidimensional array. |
| api-tabNew | Create multidimensional arrays |
| api-tabX | Interface - operations on multidimensional arrays. |
| api-tabX_ | Table operations implemented in c++ |
| api_tabSlice | Array slices |
| array-simulate | Simulate data from array. |
| as.adjMAT | Functions from Graphical Modelling with R book |
| as.parray | Representation of and operations on multidimensional arrays |
| ashtrees | Crown dieback in ash trees |
-- B --
| BodyFat | Body Fat Data |
| breastcancer | Gene expression signatures for p53 mutation status in 250 breast cancer samples |
-- C --
| cad1 | Coronary artery disease data |
| cad2 | Coronary artery disease data |
| carcass | Lean meat contents of 344 pig carcasses |
| carcassall | Lean meat contents of 344 pig carcasses |
| cell2entry | Table cell operations. |
| cell2entry_ | Low level table cell operations implemented in c++ |
| cell2entry_perm | Table cell operations. |
| cell2entry_perm_ | Low level table cell operations implemented in c++ |
| chestSim1000 | Simulated data from the Chest Clinic example |
| chestSim10000 | Simulated data from the Chest Clinic example |
| chestSim100000 | Simulated data from the Chest Clinic example |
| chestSim500 | Simulated data from the Chest Clinic example |
| chestSim50000 | Simulated data from the Chest Clinic example |
| children | Query a graph |
| closure | Query a graph |
| coerceGraph | Graph coercion |
| colmat2list | gRbase utilities |
| colSumsPrim | gRbase utilities |
| colwiseProd | gRbase utilities |
| combn_prim | Generate All Combinations of n Elements Taken m at a Time |
| compareModels | Generic function for model comparison |
| compile | Compile and propagate functions |
| conc2pcor | Partial correlation (matrix) |
| connComp | Query a graph |
| cov2pcor | Partial correlation (matrix) |
-- D --
| dag | Create undirected and directed graphs |
| dag2edge_matrix | Coerce dag to edge matrix |
| dagi | Create undirected and directed graphs |
| dagList | Create undirected and directed graphs |
| data-ashtrees | Crown dieback in ash trees |
| data-BodyFat | Body Fat Data |
| data-breastcancer | Gene expression signatures for p53 mutation status in 250 breast cancer samples |
| data-carcass | Lean meat contents of 344 pig carcasses |
| data-chestSim | Simulated data from the Chest Clinic example |
| data-dietox | Growth curves of pigs in a 3x3 factorial experiment |
| data-dumping | Gastric Dumping |
| data-lizard | Lizard behaviour |
| data-mathmark | Mathematics marks for students |
| data-mildew | Mildew fungus |
| data-milkcomp | Milk composition data |
| data-Nutrimouse | The Nutrimouse Dataset |
| data-personality | Personality traits |
| data-rats | Weightloss of rats |
| data-reinis | Risk factors for coronary heart disease. |
| data-wine | Chemical composition of wine |
| data2parray | Representation of and operations on multidimensional arrays |
| data_cad | Coronary artery disease data |
| data_handling | Utilities for data handling |
| dietox | Growth curves of pigs in a 3x3 factorial experiment |
| dimnames_match | Check if object is array |
| downstream-aliases | Downstream aliases |
| dropEdge.gModel | Internal functions for the gRbase package |
| dumping | Gastric Dumping |
-- E --
| edgeList | Find edges in a graph and edges not in a graph. |
| edgeListMAT | Find edges in a graph and edges not in a graph. |
| edges | Query a graph |
| edges_ | Query a graph |
| edge_matrix | Coerce dag to edge matrix |
| edge_matrix2dag | Coerce dag to edge matrix |
| ell | Downstream aliases |
| ellK | Downstream aliases |
| entry2cell | Table cell operations. |
| entry2cell_ | Low level table cell operations implemented in c++ |
| extract.power | Internal functions for the gRbase package |
-- F --
| fact_grid | Table cell operations. |
| fastcombn | Generate All Combinations of n Elements Taken m at a Time |
| filter_maximal_vectors | Suite of set operations |
| fit | Compile and propagate functions |
-- G --
| getCliques | Get cliques of an undirected graph |
| get_cliques | Get cliques of an undirected graph |
| get_subset | Suite of set operations |
| get_superset | Suite of set operations |
| ggm | Internal functions for the gRbase package |
| gmwr_book | Functions from Graphical Modelling with R book |
| graph-clique | Get cliques of an undirected graph |
| graph-coerce | Graph coercion |
| graph-coerce-api | API for coercing graph representations |
| graph-create | Create undirected and directed graphs |
| graph-edgeList | Find edges in a graph and edges not in a graph. |
| graph-gcproperties | Properties of a generating class (for defining a graph). |
| graph-mcs | Maximum cardinality search on undirected graph. |
| graph-min-triangulate | Minimal triangulation of an undirected graph |
| graph-moralize | Moralize a directed acyclic graph |
| graph-mpd | Maximal prime subgraph decomposition |
| graph-randomdag | Random directed acyclic graph |
| graph-rip | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| graph-triangulate | Triangulation of an undirected graph |
| graph_as | Graph coercion |
| graph_coerce_list | Coercion of graphs represented as lists |
| graph_iplot | Function for plotting graphs using the 'igraph' package. |
| graph_is | Check properties of graphs. |
| graph_query | Query a graph |
| graph_topo_sort | Topological sort of vertices in directed acyclic graph |
| graph_vpar | List of vertices and their parents for graph. |
| gRbase | The package 'gRbase': summary information |
| grbase-utilities | gRbase utilities |
| grbase_generics | Compile and propagate functions |
| g_adl2dm_ | Coercion of graphs represented as lists |
| g_adl2ig_ | Coercion of graphs represented as lists |
| g_adl2M_ | Coercion of graphs represented as lists |
| g_adl2sm_ | Coercion of graphs represented as lists |
| g_adl2XX_ | Coercion of graphs represented as lists |
| g_dagl2dm_ | Coercion of graphs represented as lists |
| g_dagl2ig_ | Coercion of graphs represented as lists |
| g_dagl2M_ | Coercion of graphs represented as lists |
| g_dagl2sm_ | Coercion of graphs represented as lists |
| g_dagl2XX_ | Coercion of graphs represented as lists |
| g_dm2ig_ | API for coercing graph representations |
| g_dm2sm_ | API for coercing graph representations |
| g_ig2dm_ | API for coercing graph representations |
| g_ig2sm_ | API for coercing graph representations |
| g_M2adl_ | Coercion of graphs represented as lists |
| g_M2dagl_ | Coercion of graphs represented as lists |
| g_M2ugl_ | Coercion of graphs represented as lists |
| g_sm2dm_ | API for coercing graph representations |
| g_sm2ig_ | API for coercing graph representations |
| g_ugl2dm_ | Coercion of graphs represented as lists |
| g_ugl2ig_ | Coercion of graphs represented as lists |
| g_ugl2M_ | Coercion of graphs represented as lists |
| g_ugl2sm_ | Coercion of graphs represented as lists |
| g_ugl2XX_ | Coercion of graphs represented as lists |
| g_xm2dm_ | API for coercing graph representations |
| g_xm2ig_ | API for coercing graph representations |
| g_xm2sm_ | API for coercing graph representations |
| g_xm2xm_ | API for coercing graph representations |
-- I --
| internal | Internal functions for the gRbase package |
| intersectPrim | Internal functions for the gRbase package |
| iplot | Function for plotting graphs using the 'igraph' package. |
| iplot.igraph | Function for plotting graphs using the 'igraph' package. |
| is.adjMAT | Check properties of graphs. |
| is.complete | Query a graph |
| is.DAG | Check properties of graphs. |
| is.decomposition | Query a graph |
| is.DG | Check properties of graphs. |
| is.named.array | Check if object is array |
| is.simplicial | Query a graph |
| is.subsetof | Suite of set operations |
| is.triangulated | Query a graph |
| is.TUG | Check properties of graphs. |
| is.UG | Check properties of graphs. |
| isDecomposable | Properties of a generating class (for defining a graph). |
| isDecomposable.default | Properties of a generating class (for defining a graph). |
| isGraphical | Properties of a generating class (for defining a graph). |
| isGraphical.default | Properties of a generating class (for defining a graph). |
| isGSD_glist | Internal functions for the gRbase package |
| is_adjMAT | Check properties of graphs. |
| is_dag | Check properties of graphs. |
| is_dagMAT | Check properties of graphs. |
| is_dg | Check properties of graphs. |
| is_dgMAT | Check properties of graphs. |
| is_dimnames_ | Check if object is array |
| is_inset | Suite of set operations |
| is_named_array_ | Check if object is array |
| is_number_vector_ | Check if object is array |
| is_subsetof | Suite of set operations |
| is_tug | Check properties of graphs. |
| is_tugMAT | Check properties of graphs. |
| is_ug | Check properties of graphs. |
| is_ugMAT | Check properties of graphs. |
-- J --
| jTree | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| junctionTree | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| junction_tree | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| junction_tree.default | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| junction_treeMAT | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
-- L --
| lapplyI2V | gRbase utilities |
| lapplyV2I | gRbase utilities |
| list2rhsf | gRbase utilities |
| list2rhsFormula | gRbase utilities |
| listify_dots | gRbase utilities |
| lizard | Lizard behaviour |
| lizardAGG | Lizard behaviour |
| lizardRAW | Lizard behaviour |
-- M --
| makeDimNames | Representation of and operations on multidimensional arrays |
| make_plevels_ | Low level table cell operations implemented in c++ |
| MAT2ftM_ | Internal functions for the gRbase package |
| matchPrim | Internal functions for the gRbase package |
| math | Mathematics marks for students |
| mathmark | Mathematics marks for students |
| matrix2list | gRbase utilities |
| maxClique | Get cliques of an undirected graph |
| maxCliqueMAT | Get cliques of an undirected graph |
| maximal_sets | Suite of set operations |
| max_cliqueMAT | Get cliques of an undirected graph |
| mcs | Maximum cardinality search on undirected graph. |
| mcs.default | Maximum cardinality search on undirected graph. |
| mcsMAT | Maximum cardinality search on undirected graph. |
| mcs_marked | Maximum cardinality search on undirected graph. |
| mcs_marked.default | Maximum cardinality search on undirected graph. |
| mcs_markedMAT | Maximum cardinality search on undirected graph. |
| mildew | Mildew fungus |
| milkcomp | Milk composition data |
| milkcomp1 | Milk composition data |
| minimal_sets | Suite of set operations |
| minimal_triang | Minimal triangulation of an undirected graph |
| minimal_triangMAT | Minimal triangulation of an undirected graph |
| moralize | Moralize a directed acyclic graph |
| moralize.default | Moralize a directed acyclic graph |
| moralizeMAT | Moralize a directed acyclic graph |
| mpd | Maximal prime subgraph decomposition |
| mpd.default | Maximal prime subgraph decomposition |
| mpdMAT | Maximal prime subgraph decomposition |
-- N --
| names2pairs | Create all possible pairs |
| next_cell | Table cell operations. |
| next_cell2 | Table cell operations. |
| next_cell2_ | Low level table cell operations implemented in c++ |
| next_cell_ | Low level table cell operations implemented in c++ |
| next_cell_slice | Table cell operations. |
| next_cell_slice_ | Low level table cell operations implemented in c++ |
| nLevels | Utilities for data handling |
| nLevels.default | Utilities for data handling |
| nodes | Query a graph |
| nodes-method | Query a graph |
| nodes_ | Query a graph |
| nonEdgeList | Find edges in a graph and edges not in a graph. |
| nonEdgeListMAT | Find edges in a graph and edges not in a graph. |
| Nutrimouse | The Nutrimouse Dataset |
-- O --
| outerPrim | Internal functions for the gRbase package |
-- P --
| pairs2num | gRbase utilities |
| parents | Query a graph |
| parray | Representation of and operations on multidimensional arrays |
| perm_cell_entries | Table cell operations. |
| perm_cell_entries_ | Low level table cell operations implemented in c++ |
| personality | Personality traits |
| processFormula | Internal functions for the gRbase package |
| propagate | Compile and propagate functions |
| prostate | Prostate Tumor Gene Expression Dataset |
-- Q --
| qgraph | Query a graph |
| querygraph | Query a graph |
-- R --
| randomGraph | Internal functions for the gRbase package |
| random_dag | Random directed acyclic graph |
| rats | Weightloss of rats |
| reinis | Risk factors for coronary heart disease. |
| removeEdge | Query a graph |
| remove_redundant | Suite of set operations |
| rhsf2list | gRbase utilities |
| rhsf2vec | gRbase utilities |
| rhsFormula2list | gRbase utilities |
| rip | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| rip.default | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| ripMAT | Create RIP ordering of the cliques of an undirected graph; create junction tree. |
| rowmat2list | gRbase utilities |
| rowSumsPrim | gRbase utilities |
-- S --
| selectOrder | Internal functions for the gRbase package |
| separates | Query a graph |
| set-operations | Suite of set operations |
| setdiffPrim | Internal functions for the gRbase package |
| simplicialNodes | Query a graph |
| simulate.array | Simulate data from array. |
| simulate.table | Simulate data from array. |
| simulate.xtabs | Simulate data from array. |
| simulateArray | Simulate data from array. |
| slice2entry | Table cell operations. |
| slice2entry_ | Low level table cell operations implemented in c++ |
| solveSPD | Internal functions for the gRbase package |
| stepwise | Compile and propagate functions |
| subGraph | Query a graph |
| subsetof | Suite of set operations |
| symMAT2ftM_ | Internal functions for the gRbase package |
-- T --
| tabAdd | Interface - operations on multidimensional arrays. |
| tabAlign | Interface - operations on multidimensional arrays. |
| tabDist | Marginalize and condition in multidimensional array. |
| tabDiv | Interface - operations on multidimensional arrays. |
| tabDiv0 | Interface - operations on multidimensional arrays. |
| tabEqual | Interface - operations on multidimensional arrays. |
| tabExpand | Interface - operations on multidimensional arrays. |
| tableDiv | Array operations (2007) |
| tableGetSliceIndex | Array operations (2007) |
| tableMargin | Array operations (2007) |
| tableMult | Array operations (2007) |
| tableOp | Array operations (2007) |
| tableOp0 | Array operations (2007) |
| tableOp2 | Array operations (2007) |
| tablePerm | Array operations (2007) |
| tableSetSliceValue | Array operations (2007) |
| tableSlice | Array operations (2007) |
| tableSlicePrim | Array operations (2007) |
| tabListAdd | Interface - operations on multidimensional arrays. |
| tabListMult | Interface - operations on multidimensional arrays. |
| tabMarg | Interface - operations on multidimensional arrays. |
| tabMult | Interface - operations on multidimensional arrays. |
| tabNew | Create multidimensional arrays |
| tabNormalize | Interface - operations on multidimensional arrays. |
| tabOp | Interface - operations on multidimensional arrays. |
| tabPerm | Interface - operations on multidimensional arrays. |
| tabProd | Interface - operations on multidimensional arrays. |
| tabSlice | Array slices |
| tabSlice2 | Array slices |
| tabSlice2Entries | Array slices |
| tabSliceMult | Array slices |
| tabSlicePrim | Array slices |
| tabSubt | Interface - operations on multidimensional arrays. |
| tabSum | Interface - operations on multidimensional arrays. |
| tab_add_ | Table operations implemented in c++ |
| tab_align_ | Table operations implemented in c++ |
| tab_div0_ | Table operations implemented in c++ |
| tab_div_ | Table operations implemented in c++ |
| tab_equal_ | Table operations implemented in c++ |
| tab_expand_ | Table operations implemented in c++ |
| tab_list_add_ | Table operations implemented in c++ |
| tab_list_mult_ | Table operations implemented in c++ |
| tab_marg_ | Table operations implemented in c++ |
| tab_mult_ | Table operations implemented in c++ |
| tab_op_ | Table operations implemented in c++ |
| tab_perm_ | Table operations implemented in c++ |
| tab_subt_ | Table operations implemented in c++ |
| topoSort | Topological sort of vertices in directed acyclic graph |
| topoSortMAT | Topological sort of vertices in directed acyclic graph |
| topo_sort | Topological sort of vertices in directed acyclic graph |
| topo_sortMAT | Topological sort of vertices in directed acyclic graph |
| triang | Triangulation of an undirected graph |
| triang.default | Triangulation of an undirected graph |
| triangulate | Triangulation of an undirected graph |
| triangulate.default | Triangulation of an undirected graph |
| triangulateMAT | Triangulation of an undirected graph |
| triang_elo | Triangulation of an undirected graph |
| triang_elo.default | Triangulation of an undirected graph |
| triang_eloMAT | Triangulation of an undirected graph |
| triang_eloMAT_ | Triangulation of an undirected graph |
| triang_mcwh | Triangulation of an undirected graph |
| triang_mcwh.default | Triangulation of an undirected graph |
| triang_mcwhMAT_ | Triangulation of an undirected graph |
-- U --
| ug | Create undirected and directed graphs |
| ug2dag | Coerce between undirected and directed graphs when possible |
| ugi | Create undirected and directed graphs |
| ugList | Create undirected and directed graphs |
| uniquePrim | Internal functions for the gRbase package |
| unlistPrim | Internal functions for the gRbase package |
-- V --
| valueLabels | Utilities for data handling |
| valueLabels.default | Utilities for data handling |
| varNames | Utilities for data handling |
| varNames.default | Utilities for data handling |
| vchi | List of vertices and their parents for graph. |
| vchiMAT | List of vertices and their parents for graph. |
| vpar | List of vertices and their parents for graph. |
| vparMAT | List of vertices and their parents for graph. |
-- W --
| which.arr.index | gRbase utilities |
| which_matrix_index | gRbase utilities |
| wine | Chemical composition of wine |
-- misc --
| %>% | Internal functions for the gRbase package |
| %a*% | Array algebra |
| %a+% | Array algebra |
| %a-% | Array algebra |
| %a/% | Array algebra |
| %a/0% | Array algebra |
| %a==% | Array algebra |
| %aalign% | Array algebra |
| %amarg% | Array algebra |
| %aperm% | Array algebra |
| %aslice% | Array algebra |
| %aslice*% | Array algebra |
| %a^% | Array algebra |
| %a_% | Array algebra |