gRbase: A package for graphical modelling in R

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.

AuthorSren Hjsgaard <sorenh@math.aau.dk> with contributions from Claus Dethlefsen <cld@rn.dk> and Clive Bowsher <C.Bowsher@statslab.cam.ac.uk>
Date of publication2013-01-30 11:39:10
MaintainerSren Hjsgaard <sorenh@math.aau.dk>
LicenseGPL (>= 2)
Version1.6-7
http://people.math.aau.dk/~sorenh/software/gR/

View on R-Forge

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

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