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gRbase

A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of 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. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details. NOTICE 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.

Functions (65)

ZOLD-gModel

Old: Class "gModel" - graphical models

ZOLD-gRfit

Old: Class "gRfit" - fitted graphical models

ZOLD-gmData

Old: Class "gmData" graphical meta data

ZOLD-hllm

Old: Hierarchical log-linear models

ZOLD-validVarTypes

Old: Admissible variable types in gmData objects

all-subsets

Create all subsets

all_pairs

Create all possible pairs

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.

compareModels

Generic function for model comparison

cov2pcor

Partial correlation (matrix)

data-BodyFat

Body Fat Data

data-Nutrimouse

The Nutrimouse Dataset

data-ashtrees

Crown dieback in ash trees

data-breastcancer

Gene expression signatures for p53 mutation status in 250 breast cancer samples

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-rats

Weightloss of rats

data-reinis

Risk factors for coronary heart disease.

data-wine

Chemical composition of wine

downstream-aliases

Downstream aliases

fastcombn

Generate All Combinations of n Elements Taken m at a Time

gRbase

The package ‘gRbase’: summary information

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-ug2dag

Coerce between undirected and directed graphs when possible

graph-vpar

List of vertices and their parents for graph.

grbase-utilities

gRbase utilities

grbase_generics

Compile and propagate functions

internal

Internal functions for the gRbase package

set-operations

Suite of set operations

gRbase

A Package for Graphical Modelling in R

v1.8-6.7

GPL (>= 2)

Authors

Søren Højsgaard <sorenh@math.aau.dk>

Initial release

gRbase

Functions (65)

gRbase

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