# A Package for Graphical Modelling in R

## Documentation for package ‘gRbase’ version 1.8-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## 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 --

adjList2adjMAT | Graph, matrix and generating class coercions
adjList2M | Graph, matrix and generating class coercions
ancestors | Query a graph
ancestralGraph | Query a graph
ancestralSet | Query a graph
array-algebra | Array algebra
array-create | Create multidimensional arrays
array-dimnames | Check compatibility of dimnames
array-distribution | Marginalize and condition in multidimensional array.
array-normalize | Normalize an array
array-operations | Operations on multidimensional arrays.
array-properties | Check if object is array
array-slice | Array slices
ar_add | Array algebra
ar_align | Operations on multidimensional arrays.
ar_dist | Marginalize and condition in multidimensional array.
ar_div | Array algebra
ar_div0 | Array algebra
ar_equal | Operations on multidimensional arrays.
ar_expand | Operations on multidimensional arrays.
ar_marg | Operations on multidimensional arrays.
ar_mult | Array algebra
ar_new | Create multidimensional arrays
ar_normalize | Normalize an array
ar_perm | Operations on multidimensional arrays.
ar_prod | Array algebra
ar_prod_list | Operations on multidimensional arrays.
ar_slice | Array slices
ar_slice_entries | Array slices
ar_slice_mult | Array slices
ar_slice_prim | Array slices
ar_subt | Array algebra
ar_sum | Array algebra
ar_sum_list | Operations on multidimensional arrays.
as.adjMAT | Graph, matrix and generating class coercions
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 --

cad | Coronary artery disease data
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
chestSim | Simulated data from the Chest Clinic example
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
coerceGraph.dgCMatrix | Graph coercion
coerceGraph.graphNEL | Graph coercion
coerceGraph.igraph | Graph coercion
coerceGraph.matrix | Graph coercion
colwiseProd | Utility functions for gRbase
combnPrim | 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)
cov2pcor | Partial correlation (matrix)

## -- D --

dag | Create undirected and directed graphs
dagList | Create undirected and directed graphs
dagList2dgCMatrix | Create undirected and directed graphs
dagList2graphNEL | Graph, matrix and generating class coercions
dagList2M | Graph, matrix and generating class coercions
dagList2matrix | Create undirected and directed graphs
dagList2tfM | Graph, matrix and generating class coercions
data2parray | Representation of and operations on multidimensional arrays
df2xtabs | Create multidimensional arrays
dietox | Growth curves of pigs in a 3x3 factorial experiment
dimnames_match | Check compatibility of dimnames
dimnames_match_ | Check compatibility of dimnames
dumping | Gastric Dumping

## -- E --

edgeList | Find edges in a graph and edges not in a graph.
edgeList.default | Find edges in a graph and edges not in a graph.
edgeListMAT | Find edges in a graph and edges not in a graph.

## -- F --

fit | Compile and propagate functions

## -- G --

getCliques | Get cliques of an undirected graph
getCliques.default | Get cliques of an undirected graph
getCliques.graphNEL | Get cliques of an undirected graph
get_subset_ | Utility functions for gRbase
get_superset_ | Utility functions for gRbase
glist2adjMAT | Graph, matrix and generating class coercions
graph-cliques | Get cliques of an undirected graph
graph-coerce | Graph coercion
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-iplot | Function for plotting graphs using the 'igraph' package.
graph-is | Check properties of graphs.
graph-mcs | Maximum cardinality search on undirected graph.
graph-minimaltriang | Minimal triangulation of an undirected graph
graph-moralize | Moralize a directed acyclic graph
graph-mpd | Maximal prime subgraph decomposition
graph-query | Query a graph
graph-randomdag | Random directed acyclic graph
graph-rip | Create RIP ordering of the cliques of an undirected graph; create junction tree.
graph-toposort | Topological sort of vertices in directed acyclic graph
graph-triang | Triangulation of an undirected graph
graph-triangulate | Triangulation of an undirected graph
graph-vpar | List of vertices and their parents for graph.
graph-xxx2yyy | Graph, matrix and generating class coercions
graphNEL2adjMAT | Graph, matrix and generating class coercions
graphNEL2dgCMatrix | Graph, matrix and generating class coercions
graphNEL2ftM | Graph, matrix and generating class coercions
graphNEL2igraph | Graph, matrix and generating class coercions
graphNEL2M | Graph, matrix and generating class coercions
graphNEL2MAT | Graph, matrix and generating class coercions
graphNEL2matrix | Graph, matrix and generating class coercions
graphNEL2tfM | Graph, matrix and generating class coercions
gRbase | The package 'gRbase': summary information
gRbase-generics | Compile and propagate functions

## -- I --

iplot | Function for plotting graphs using the 'igraph' package.
iplot.graphNEL | 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.DAG.default | Check properties of graphs.
is.DAG.graphNEL | Check properties of graphs.
is.DAGMAT | Check properties of graphs.
is.decomposition | Query a graph
is.DG | Check properties of graphs.
is.DG.default | Check properties of graphs.
is.DG.graphNEL | Check properties of graphs.
is.DGMAT | Check properties of graphs.
is.insetlist | Set operations
is.named.array | Check if object is array
is.simplicial | Query a graph
is.subsetof | Set operations
is.TUG | Check properties of graphs.
is.TUG.default | Check properties of graphs.
is.TUG.graphNEL | Check properties of graphs.
is.TUGMAT | Check properties of graphs.
is.UG | Check properties of graphs.
is.UG.default | Check properties of graphs.
is.UG.graphNEL | Check properties of graphs.
is.UGMAT | 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)
isin | Set operations
is_dimnames_ | Check if object is array
is_named_array_ | Check if object is array
is_number_vector_ | Check if object is array
is_subsetof_ | Utility functions for gRbase

## -- J --

jTree | Create RIP ordering of the cliques of an undirected graph; create junction tree.
jTree.default | Create RIP ordering of the cliques of an undirected graph; create junction tree.
jTreeMAT | 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.
junctionTree.default | Create RIP ordering of the cliques of an undirected graph; create junction tree.
junctionTreeMAT | Create RIP ordering of the cliques of an undirected graph; create junction tree.

## -- L --

lizard | Lizard behaviour
lizardAGG | Lizard behaviour
lizardRAW | Lizard behaviour

## -- M --

M2adjList | Graph, matrix and generating class coercions
M2dagList | Graph, matrix and generating class coercions
M2graphNEL | Graph, matrix and generating class coercions
M2igraph | Graph, matrix and generating class coercions
M2ugList | Graph, matrix and generating class coercions
MAT2dgCMatrix | Graph, matrix and generating class coercions
MAT2matrix | Graph, matrix and generating class coercions
math | Mathematics marks for students
mathmark | Mathematics marks for students
maxCliqueMAT | Get cliques of an undirected graph
maximalSets | Set operations
mcs | Maximum cardinality search on undirected graph.
mcs.default | Maximum cardinality search on undirected graph.
mcsmarked | Maximum cardinality search on undirected graph.
mcsmarked.default | Maximum cardinality search on undirected graph.
mcsmarkedMAT | Maximum cardinality search on undirected graph.
mcsMAT | Maximum cardinality search on undirected graph.
mildew | Mildew fungus
milkcomp | Milk composition data
milkcomp1 | Milk composition data
minimalSets | Set operations
minimalTriang | Minimal triangulation of an undirected graph
minimalTriang.default | Minimal triangulation of an undirected graph
minimalTriangMAT | 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 --

newar | Create multidimensional arrays
nonEdgeList | Find edges in a graph and edges not in a graph.
nonEdgeList.default | 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 --

old-array-operations | Array operations (2007)
old-parray | Representation of and operations on multidimensional arrays

## -- P --

parents | Query a graph
parray | Representation of and operations on multidimensional arrays
propagate | Compile and propagate functions

## -- Q --

querygraph | Query a graph

## -- R --

random_dag | Random directed acyclic graph
rats | Weightloss of rats
reinis | Risk factors for coronary heart disease.
removeRedundant | Set operations
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.

## -- S --

simplicialNodes | Query a graph
simulateArray | Simulate data from array.
stepwise | Compile and propagate functions
subsetof | Set operations

## -- T --

tab | Create multidimensional arrays
tabAdd | Array algebra
tabAdd__ | Operations on multidimensional arrays.
tabAlign | Operations on multidimensional arrays.
tabAlign__ | Operations on multidimensional arrays.
tabCondProb | Operations on multidimensional arrays.
tabDist | Marginalize and condition in multidimensional array.
tabDiv | Array algebra
tabDiv0 | Array algebra
tabDiv0__ | Operations on multidimensional arrays.
tabDiv__ | Operations on multidimensional arrays.
tabEqual | Operations on multidimensional arrays.
tabEqual__ | Operations on multidimensional arrays.
tabExpand | Operations on multidimensional arrays.
tabExpand__ | Operations on multidimensional arrays.
tabExt | Operations on multidimensional arrays.
tableDiv | Array operations (2007)
tableGetSliceIndex | Array operations (2007)
tableMargin | Array operations (2007)
tableMult | Array operations (2007)
tableOp | Array operations (2007)
tableOp2 | Array operations (2007)
tablePerm | Array operations (2007)
tableSetSliceValue | Array operations (2007)
tableSlice | Array operations (2007)
tableSlicePrim | Array operations (2007)
tabListAdd | Operations on multidimensional arrays.
tabListAdd__ | Operations on multidimensional arrays.
tabListMult | Operations on multidimensional arrays.
tabListMult__ | Operations on multidimensional arrays.
tabMarg | Operations on multidimensional arrays.
tabMarg__ | Operations on multidimensional arrays.
tabMult | Array algebra
tabMult__ | Operations on multidimensional arrays.
tabNormalize | Normalize an array
tabOp__ | Operations on multidimensional arrays.
tabPerm | Operations on multidimensional arrays.
tabPerm__ | Operations on multidimensional arrays.
tabProd | Array algebra
tabSlice | Operations on multidimensional arrays.
tabSlice2 | Operations on multidimensional arrays.
tabSlice2Entries | Operations on multidimensional arrays.
tabSlice2Entries_ | Operations on multidimensional arrays.
tabSliceMult | Operations on multidimensional arrays.
tabSlicePrim | Operations on multidimensional arrays.
tabSubt | Array algebra
tabSubt__ | Operations on multidimensional arrays.
tabSum | Array algebra
topoSort | Topological sort of vertices in directed acyclic graph
topoSort.default | Topological sort of vertices in directed acyclic graph
topoSortMAT | Topological sort of vertices in directed acyclic graph
topoSort_vparList | 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

## -- U --

ug | Create undirected and directed graphs
ug2dag | Graph, matrix and generating class coercions
ugList | Create undirected and directed graphs
ugList2dgCMatrix | Create undirected and directed graphs
ugList2graphNEL | Graph, matrix and generating class coercions
ugList2M | Graph, matrix and generating class coercions
ugList2matrix | Create undirected and directed graphs

## -- V --

vchi | List of vertices and their parents for graph.
vchi.graphNEL | List of vertices and their parents for graph.
vchi.Matrix | List of vertices and their parents for graph.
vchi.matrix | List of vertices and their parents for graph.
vchiMAT | List of vertices and their parents for graph.
vpaL2tfM | Graph, matrix and generating class coercions
vpaList2adjMAT | Graph, matrix and generating class coercions
vpar | List of vertices and their parents for graph.
vpar.graphNEL | List of vertices and their parents for graph.
vpar.Matrix | List of vertices and their parents for graph.
vpar.matrix | List of vertices and their parents for graph.
vparMAT | List of vertices and their parents for graph.

## -- W --

wine | Chemical composition of wine

## -- misc --

%a*% | Array algebra
%a+% | Array algebra
%a-% | Array algebra
%a/% | Array algebra
%a/0% | Array algebra
%a==% | Operations on multidimensional arrays.
%a^% | Operations on multidimensional arrays.
%a_% | Operations on multidimensional arrays.