A Package for Graphical Modelling in R

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Documentation for package ‘gRbase’ version 2.0.2

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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