gRbase: A package for graphical modelling in R

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The gRbase package provides certain general constructs which are used by other graphical modelling packages, in particular by the packages gRain, gRim and gRc. . gRbase contains several datasets relevant for use in connection with graphical models. Almost all datasets 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) junctionTree. . gRbase facilities for array operations, . gRbase implements functions for testing for conditional independence. . gRbase illustrates how hierarchical log-linear models (hllm) may be implemented and describes concept of gmData (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.

Author
Sren Hjsgaard <sorenh@math.aau.dk> with contributions from Claus Dethlefsen <cld@rn.dk> and Clive Bowsher <C.Bowsher@statslab.cam.ac.uk>
Date of publication
2013-01-30 11:39:10
Maintainer
Sren Hjsgaard <sorenh@math.aau.dk>
License
GPL (>= 2)
Version
1.6-7
URLs

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Man pages

arrayCombine
Combine arrays
combnPrim
Generate All Combinations of n Elements Taken m at a Time
compareModels
Generic function for model comparison
compile-propagate
Compile and propagate functions
cov2pcor
Partial correlation (matrix)
DATA-ashtrees
Crown dieback in ash trees
DATA-BodyFat
Body Fat Data
DATA-breastcancer
Gene expression signatures for p53 mutation status in 250...
DATA-cad
Coronary artery disease data
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-rats
Weightloss of rats
DATA-reinis
Risk factors for coronary heart disease.
DATA-wine
Chemical composition of wine
GraphAlgo-edgeList
Find edges in a graph and edges not in a graph.
GraphAlgo-glist2adjMAT
Creates adjacency matrix for a graph from a list of...
GraphAlgo-is-graph
Check properties of graphs.
GraphAlgo-mcs
Maximum cardinality search on undirected graph.
GraphAlgo-minimalTriang
Minimal triangulation of an undirected graph
GraphAlgo-moralize
Moralize a directed acyclic graph
GraphAlgo-mpd
Maximal prime subgraph decomposition
GraphAlgo-operations1
Simple operations on undirected and directed acyclic graphs.
GraphAlgo-querygraph
Query a graph
GraphAlgo-rip
RIP ordering and junction tree.
GraphAlgo-topoSort
Topological sort of vertices in directed
GraphAlgo-triangulate
Triangulation of an undirected graph
GraphAlgo-vpar
List of vertices and their parents for graph.
gRbase
The package 'gRbase': summary information
gRbase-internal
Internal gRbase functions
gRbase-utilities
Utility functions for gRbase
iplot
Function for plotting graphs using the 'igraph' package.
parray
Representation of and operations on multidimensional tables
randomDag
Random directed acyclic graph
removeRedundant
Set operations
table-operations
Compute table margin or table slice
ugdag
Create undirected and directed graphs
ZOLD-gmData
Class "gmData" graphical meta data
ZOLD-gModel
Class "gModel" - graphical models
ZOLD-gRfit
Class "gRfit" - fitted graphical models
ZOLD-hllm
Hierarchical log-linear models
ZOLD-validVarTypes
Admissible variable types in gmData objects

Files in this package

gRbase
gRbase/data
gRbase/data/wine.txt.bz2
gRbase/data/rats.txt.gz
gRbase/data/milkcomp1.txt.bz2
gRbase/data/milkcomp.txt.bz2
gRbase/data/mathmark.txt.bz2
gRbase/data/math.txt.bz2
gRbase/data/lizardRAW.txt.bz2
gRbase/data/lizardAGG.txt.gz
gRbase/data/dietox.txt.xz
gRbase/data/carcassall.txt.bz2
gRbase/data/carcass.txt.bz2
gRbase/data/cad2.txt.bz2
gRbase/data/cad1.txt.bz2
gRbase/data/BodyFat.txt.bz2
gRbase/data/datalist
gRbase/data/chestSim100000.RData
gRbase/data/reinis.RData
gRbase/data/chestSim10000.RData
gRbase/data/chestSim500.RData
gRbase/data/breastcancer.RData
gRbase/data/Nutrimouse.RData
gRbase/data/chestSim1000.RData
gRbase/data/lizard.RData
gRbase/data/ashtrees.RData
gRbase/data/dumping.RData
gRbase/data/chestSim50000.RData
gRbase/data/mildew.RData
gRbase/R
gRbase/R/dualRep.R
gRbase/R/GraphAlgo-moralize.R
gRbase/R/ZOLD-ggm.R
gRbase/R/graphAlgo-triangulateMAT-C.R
gRbase/R/xxxPrim.R
gRbase/R/arrayCombine.R
gRbase/R/graphAlgo-topoSortMAT-C.R
gRbase/R/AddDropEdges.R
gRbase/R/GraphAlgo-ugdag.R
gRbase/R/yyyPrim.R
gRbase/R/ZOLD-gRfit.R
gRbase/R/GraphAlgo-mcsmarked.R
gRbase/R/GraphAlgo-isGSD.R
gRbase/R/dgCMatrix.R
gRbase/R/Generics.R
gRbase/R/solveSPD.R
gRbase/R/iplot.R
gRbase/R/GraphAlgo-cliqueMAT.R
gRbase/R/GraphAlgo-minimalTriang.R
gRbase/R/GraphAlgo-vpar.R
gRbase/R/GraphAlgo-edgeList.R
gRbase/R/random_dag.R
gRbase/R/arrayops.R
gRbase/R/sparseM.R
gRbase/R/FIX-stepwise.R
gRbase/R/processFormula.R
gRbase/R/ZOLD-gModel.R
gRbase/R/GraphAlgo-is-graph.R
gRbase/R/parray.R
gRbase/R/table-operations.R
gRbase/R/globals.R
gRbase/R/asdgCMatrix-C.R
gRbase/R/zzz.R
gRbase/R/GraphAlgo-rip.R
gRbase/R/gRbase-utilities.R
gRbase/R/GraphAlgo-coerce.R
gRbase/R/setopsC.R
gRbase/R/ZOLD-gmData.R
gRbase/R/GraphAlgo-MPD.R
gRbase/R/ZOLD-hllm.R
gRbase/R/names2pairs.R
gRbase/R/ZOLD-update_gModel.R
gRbase/R/graphAlgo-topoSort.R
gRbase/R/combnPrimR.R
gRbase/R/GraphAlgo-querygraph.R
gRbase/R/graphAlgo-mcsMAT-C.R
gRbase/R/FIX-formulae.R
gRbase/R/GraphAlgo-mcs.R
gRbase/R/GraphAlgo-JunctionTree.R
gRbase/R/GraphAlgo-xxx2adjmat.R
gRbase/R/graphAlgo-triangulate.R
gRbase/R/setopsR.R
gRbase/NAMESPACE
gRbase/inst
gRbase/inst/CITATION
gRbase/inst/doc
gRbase/inst/doc/gRbase-arrayops2.Rnw
gRbase/inst/doc/gRbase-graphs.Rnw
gRbase/inst/doc/fulldef.bib
gRbase/inst/doc/gRbase-arrayops2.pdf
gRbase/inst/doc/gRbase-arrayops1.Rnw
gRbase/inst/doc/gRbase-arrayops1.pdf
gRbase/inst/doc/gRbase-graphs.pdf
gRbase/inst/doc/gRbase.bib
gRbase/DESCRIPTION
gRbase/ChangeLog
gRbase/gRbase-Ex.R
gRbase/man
gRbase/man/DATA-reinis.Rd
gRbase/man/GraphAlgo-edgeList.Rd
gRbase/man/DATA-milkcomp.Rd
gRbase/man/DATA-mildew.Rd
gRbase/man/DATA-cad.Rd
gRbase/man/ZOLD-gRfit.Rd
gRbase/man/ZOLD-gModel.Rd
gRbase/man/DATA-Nutrimouse.Rd
gRbase/man/ZOLD-hllm.Rd
gRbase/man/DATA-dumping.Rd
gRbase/man/DATA-dietox.Rd
gRbase/man/cov2pcor.Rd
gRbase/man/parray.Rd
gRbase/man/GraphAlgo-querygraph.Rd
gRbase/man/gRbase-utilities.Rd
gRbase/man/ZOLD-gmData.Rd
gRbase/man/table-operations.Rd
gRbase/man/DATA-carcass.Rd
gRbase/man/GraphAlgo-topoSort.Rd
gRbase/man/randomDag.Rd
gRbase/man/combnPrim.Rd
gRbase/man/ZOLD-validVarTypes.Rd
gRbase/man/GraphAlgo-operations1.Rd
gRbase/man/GraphAlgo-glist2adjMAT.Rd
gRbase/man/GraphAlgo-triangulate.Rd
gRbase/man/gRbase.Rd
gRbase/man/iplot.Rd
gRbase/man/compareModels.Rd
gRbase/man/GraphAlgo-rip.Rd
gRbase/man/DATA-mathmark.Rd
gRbase/man/GraphAlgo-minimalTriang.Rd
gRbase/man/DATA-BodyFat.Rd
gRbase/man/GraphAlgo-mpd.Rd
gRbase/man/DATA-rats.Rd
gRbase/man/ugdag.Rd
gRbase/man/arrayCombine.Rd
gRbase/man/GraphAlgo-vpar.Rd
gRbase/man/GraphAlgo-mcs.Rd
gRbase/man/DATA-lizard.Rd
gRbase/man/gRbase-internal.Rd
gRbase/man/DATA-ashtrees.Rd
gRbase/man/GraphAlgo-moralize.Rd
gRbase/man/GraphAlgo-is-graph.Rd
gRbase/man/DATA-breastcancer.Rd
gRbase/man/compile-propagate.Rd
gRbase/man/DATA-wine.Rd
gRbase/man/removeRedundant.Rd
gRbase/man/DATA-chestSim.Rd
gRbase/src
gRbase/src/_utils_setops.c
gRbase/src/asdgCMatrix.cpp
gRbase/src/arrayops.c
gRbase/src/spdinv-arma.cpp
gRbase/src/triangulateMAT.cpp
gRbase/src/combnC.c
gRbase/src/xxxPrim.c
gRbase/src/mcsMAT1.cpp
gRbase/src/MakevarsOLD
gRbase/src/combnPrimC.h
gRbase/src/Makevars
gRbase/src/sparseM.cpp
gRbase/src/_utils_print.c
gRbase/src/Makevars.win
gRbase/src/f2c.h
gRbase/src/combnPrimC.c
gRbase/src/topoSortMAT.cpp
gRbase/src/_utils_print.h
gRbase/todo.txt
gRbase/demo
gRbase/demo/carcass.R
gRbase/demo/haireye.R
gRbase/demo/reinis.R
gRbase/demo/00Index
gRbase/demo/cadcomplete.R
gRbase/demo/gmData.R