gRbase: A Package for Graphical Modelling in R

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The 'gRbase' package provides general features which are used by other graphical modelling packages, in particular by the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' contains several data sets relevant for use in connection with graphical models. Almost all data sets used in the book Graphical Models with R (2012) are contained in 'gRbase'. 'gRbase' implements several graph algorithms (based mainly on representing graphs as adjacency matrices - either in the form of a standard matrix or a sparse matrix). Some graph algorithms are: (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralize. (iii) triangulate. (iv) junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. These features, however, are not maintained anymore and remains in 'gRbase' only because there exists a paper describing these facilities: A Common Platform for Graphical Models in R: The 'gRbase' Package, Journal of Statistical Software, Vol 14, No 17, 2005. NOTICE Proper functionality of 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.

Author
Søren Højsgaard <sorenh@math.aau.dk>
Date of publication
2016-10-17 00:46:21
Maintainer
Søren Højsgaard <sorenh@math.aau.dk>
License
GPL (>= 2)
Version
1.8-1
URLs

View on CRAN

Man pages

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.
arraypack-internal
Internal arraypack functions
array-properties
Check if object is array
array-slice
Array slices
ashtrees
Crown dieback in ash trees
BodyFat
Body Fat Data
breastcancer
Gene expression signatures for p53 mutation status in 250...
cad
Coronary artery disease data
carcass
Lean meat contents of 344 pig carcasses
chestSim
Simulated data from the Chest Clinic example
combnPrim
Generate All Combinations of n Elements Taken m at a Time
compareModels
Generic function for model comparison
cov2pcor
Partial correlation (matrix)
dietox
Growth curves of pigs in a 3x3 factorial experiment
dumping
Gastric Dumping
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;...
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.
graph-xxx2yyy
Graph, matrix and generating class coercions
gRbase
The package 'gRbase': summary information
gRbase-generics
Compile and propagate functions
gRbase-internal
Internal gRbase functions
gRbase-utilities
Utility functions for gRbase
lizard
Lizard behaviour
mathmark
Mathematics marks for students
mildew
Mildew fungus
milkcomp
Milk composition data
Nutrimouse
The Nutrimouse Dataset
old-array-operations
Array operations (2007)
old-parray
Representation of and operations on multidimensional tables
rats
Weightloss of rats
reinis
Risk factors for coronary heart disease.
removeRedundant
Set operations
simulateArray
Simulate data from array.
wine
Chemical composition of wine
ZOLD-gmData
Old: Class "gmData" graphical meta data
ZOLD-gModel
Old: Class "gModel" - graphical models
ZOLD-gRfit
Old: Class "gRfit" - fitted graphical models
ZOLD-hllm
Old: Hierarchical log-linear models
ZOLD-validVarTypes
Old: Admissible variable types in gmData objects

Files in this package

gRbase
gRbase/TODO
gRbase/inst
gRbase/inst/CITATION
gRbase/inst/doc
gRbase/inst/doc/gRbase-graphs.Rnw
gRbase/inst/doc/gRbase-arrays.pdf
gRbase/inst/doc/gRbase-arrays.R
gRbase/inst/doc/gRbase-graphs.R
gRbase/inst/doc/gRbase-graphs.pdf
gRbase/inst/doc/gRbase-arrays.Rnw
gRbase/inst/include
gRbase/inst/include/gRbase_RcppExports.h
gRbase/inst/include/gRbase_typedefs.h
gRbase/inst/include/gRbase.h
gRbase/src
gRbase/src/_g_mcsMAT.cpp
gRbase/src/Makevars
gRbase/src/combnPrimC.h
gRbase/src/_m_matrix2dgCMatrix.cpp
gRbase/src/_g_topoSortMAT.h
gRbase/src/names2pairsM.cpp
gRbase/src/_g_mcsMAT2.cpp
gRbase/src/solveSPD.cpp
gRbase/src/combnC.c
gRbase/src/_t_tableCore.cpp
gRbase/src/_t_tableCell.cpp
gRbase/src/_utils_print.h
gRbase/src/toBeRemoved.cpp
gRbase/src/_t_array_properties.cpp
gRbase/src/_m_MAT2ftM.cpp
gRbase/src/_u_utility.cpp
gRbase/src/_m_rowmat2list.cpp
gRbase/src/_t_arrayops.c
gRbase/src/f2c.h
gRbase/src/_t_array_properties.h
gRbase/src/_g_triangulateMAT.cpp
gRbase/src/_t_tableCore.h
gRbase/src/allSubsets.cpp
gRbase/src/_t_tableClass.cpp
gRbase/src/_m_ugdag2MAT.cpp
gRbase/src/_u_setops.c
gRbase/src/_utils_print.c
gRbase/src/_u_utilities.c
gRbase/src/Makevars.win
gRbase/src/mcsMAT2.h
gRbase/src/RcppExports.cpp
gRbase/src/_g_topoSortMAT.cpp
gRbase/src/_m_isadjMAT.cpp
gRbase/src/concatenate.h
gRbase/src/_m_misc.cpp
gRbase/src/combnPrimC.c
gRbase/src/_g_rip-cliques.cpp
gRbase/src/_g_moralizeMAT.cpp
gRbase/NAMESPACE
gRbase/demo
gRbase/demo/gmData.R
gRbase/demo/carcass.R
gRbase/demo/cadcomplete.R
gRbase/demo/00Index
gRbase/demo/reinis.R
gRbase/demo/haireye.R
gRbase/data
gRbase/data/dietox.RData
gRbase/data/cad1.RData
gRbase/data/dumping.RData
gRbase/data/reinis.RData
gRbase/data/ashtrees.RData
gRbase/data/carcassall.RData
gRbase/data/carcass.RData
gRbase/data/chestSim10000.rda
gRbase/data/math.RData
gRbase/data/wine.RData
gRbase/data/chestSim100000.rda
gRbase/data/breastcancer.rda
gRbase/data/chestSim50000.rda
gRbase/data/mathmark.RData
gRbase/data/chestSim500.RData
gRbase/data/milkcomp1.RData
gRbase/data/lizard.RData
gRbase/data/Nutrimouse.rda
gRbase/data/cad2.RData
gRbase/data/milkcomp.RData
gRbase/data/mildew.RData
gRbase/data/BodyFat.RData
gRbase/data/rats.RData
gRbase/data/lizardAGG.txt.gz
gRbase/data/lizardRAW.txt.gz
gRbase/data/chestSim1000.RData
gRbase/R
gRbase/R/graph-create-ugdag.R
gRbase/R/graph-topoSort.R
gRbase/R/yyOLD-gRbase.R
gRbase/R/graph-iplot.R
gRbase/R/t_array-slice.R
gRbase/R/t_array-properties.R
gRbase/R/data-mildew.R
gRbase/R/data-rats.R
gRbase/R/graph-moralize.R
gRbase/R/graph-mcs.R
gRbase/R/processFormula.R
gRbase/R/data-dietox.R
gRbase/R/t_array-algebra-cR.R
gRbase/R/gRbase-internal.R
gRbase/R/t_array-lowlevel-ops.R
gRbase/R/t_arDist.R
gRbase/R/data-chestsim.R
gRbase/R/data-ashtrees.R
gRbase/R/graph-mpd.R
gRbase/R/graph-utilities.R
gRbase/R/data-nutrimouse.R
gRbase/R/u_setops-c.R
gRbase/R/graph-mintriang.R
gRbase/R/graph-rip.R
gRbase/R/t_array-algebra.R
gRbase/R/data-breastcancer.R
gRbase/R/t_array-parray.R
gRbase/R/u_utilities-c.R
gRbase/R/data-cad.R
gRbase/R/graph-xxx2yyy.R
gRbase/R/data-winecomp.R
gRbase/R/combnC-c.R
gRbase/R/graph-properties.R
gRbase/R/data-reinis.R
gRbase/R/t_array-create.R
gRbase/R/RcppExports.R
gRbase/R/graph-triangulate.R
gRbase/R/data-dumping.R
gRbase/R/data-bodyfat.R
gRbase/R/graph-coerce.R
gRbase/R/t_array-operations-bristol.R
gRbase/R/data-milkcomp.R
gRbase/R/gRbase-package.R
gRbase/R/graph-querygraph.R
gRbase/R/yyyPrim.R
gRbase/R/data-lizard.R
gRbase/R/data-mathmark.R
gRbase/R/cov2pcor.R
gRbase/R/t_array-operations.R
gRbase/R/gRbase-utilities-FIXME-cleanup.R
gRbase/R/t_array-simulate-R.R
gRbase/R/Generics.R
gRbase/R/data-carcass.R
gRbase/vignettes
gRbase/vignettes/gRbase-graphs.Rnw
gRbase/vignettes/fulldef.bib
gRbase/vignettes/gRbase.bib
gRbase/vignettes/gRbase-arrays.Rnw
gRbase/MD5
gRbase/build
gRbase/build/vignette.rds
gRbase/DESCRIPTION
gRbase/ChangeLog
gRbase/man
gRbase/man/cov2pcor.Rd
gRbase/man/mathmark.Rd
gRbase/man/graph-triangulate.Rd
gRbase/man/array-normalize.Rd
gRbase/man/graph-gcproperties.Rd
gRbase/man/graph-mcs.Rd
gRbase/man/wine.Rd
gRbase/man/graph-is.Rd
gRbase/man/old-array-operations.Rd
gRbase/man/graph-randomdag.Rd
gRbase/man/rats.Rd
gRbase/man/ZOLD-gmData.Rd
gRbase/man/lizard.Rd
gRbase/man/graph-create.Rd
gRbase/man/graph-rip.Rd
gRbase/man/graph-query.Rd
gRbase/man/removeRedundant.Rd
gRbase/man/reinis.Rd
gRbase/man/ZOLD-gRfit.Rd
gRbase/man/array-algebra.Rd
gRbase/man/ZOLD-validVarTypes.Rd
gRbase/man/graph-cliques.Rd
gRbase/man/compareModels.Rd
gRbase/man/gRbase-generics.Rd
gRbase/man/graph-iplot.Rd
gRbase/man/gRbase-internal.Rd
gRbase/man/simulateArray.Rd
gRbase/man/graph-minimaltriang.Rd
gRbase/man/ZOLD-hllm.Rd
gRbase/man/carcass.Rd
gRbase/man/graph-coerce.Rd
gRbase/man/gRbase.Rd
gRbase/man/graph-xxx2yyy.Rd
gRbase/man/milkcomp.Rd
gRbase/man/graph-mpd.Rd
gRbase/man/array-create.Rd
gRbase/man/arraypack-internal.Rd
gRbase/man/array-dimnames.Rd
gRbase/man/array-distribution.Rd
gRbase/man/BodyFat.Rd
gRbase/man/array-slice.Rd
gRbase/man/mildew.Rd
gRbase/man/array-properties.Rd
gRbase/man/Nutrimouse.Rd
gRbase/man/ashtrees.Rd
gRbase/man/graph-toposort.Rd
gRbase/man/combnPrim.Rd
gRbase/man/breastcancer.Rd
gRbase/man/graph-moralize.Rd
gRbase/man/cad.Rd
gRbase/man/array-operations.Rd
gRbase/man/graph-edgeList.Rd
gRbase/man/old-parray.Rd
gRbase/man/ZOLD-gModel.Rd
gRbase/man/dumping.Rd
gRbase/man/gRbase-utilities.Rd
gRbase/man/dietox.Rd
gRbase/man/chestSim.Rd
gRbase/man/graph-vpar.Rd