# A Package for Graphical Modelling in R

## Documentation for package ‘gRbase’ version 1.9.0

- 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.gModel | Internal functions for the gRbase package
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)
cov2pcor | Partial correlation (matrix)

## -- D --

dag | Create undirected and directed graphs
dag2chol | Create regression matrix matrix from DAG A DAG can be represented as a triangular matrix of regression coefficients.
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
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.
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
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-coerce-list | Coercion of graphs represented as lists
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-min-triangulate | 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-triangulate | Triangulation of an undirected graph
graph-vpar | List of vertices and their parents for graph.
graphNEL2adjMAT | API for coercing graph representations
graphNEL2M | API for coercing graph representations
graph_as | Graph coercion
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_adl2gn_ | 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_dagl2gn_ | 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_dm2gn_ | API for coercing graph representations
g_dm2ig_ | API for coercing graph representations
g_dm2sm_ | API for coercing graph representations
g_gn2dm_ | API for coercing graph representations
g_gn2ftM_ | API for coercing graph representations
g_gn2ig_ | API for coercing graph representations
g_gn2sm_ | API for coercing graph representations
g_gn2tfM_ | API for coercing graph representations
g_gn2xm_ | API for coercing graph representations
g_ig2dm_ | API for coercing graph representations
g_ig2gn_ | 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_sm2gn_ | API for coercing graph representations
g_sm2ig_ | API for coercing graph representations
g_ugl2dm_ | Coercion of graphs represented as lists
g_ugl2gn_ | 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_xm2gn_ | 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.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.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.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 --

M2graphNEL | API for coercing graph representations
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
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++
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

## -- 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.
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
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
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 --

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