ggm: Functions for graphical Markov models

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Functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.

Author
Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Date of publication
2015-01-21 12:47:19
Maintainer
Giovanni M. Marchetti <giovanni.marchetti@disia.unifi.it>
License
GPL (>= 2)
Version
2.3

View on CRAN

Man pages

adjMatrix
Adjacency matrix of a graph
AG
Ancestral graph
allEdges
All edges of a graph
anger
Anger data
basiSet
Basis set of a DAG
bfsearch
Breadth first search
binve
Inverts a marginal log-linear parametrization
blkdiag
Block diagonal matrix
blodiag
Block diagonal matrix
checkIdent
Identifiability of a model with one latent variable
cmpGraph
The complementary graph
conComp
Connectivity components
correlations
Marginal and partial correlations
cycleMatrix
Fundamental cycles
DAG
Directed acyclic graphs (DAGs)
derived
Data on blood pressure body mass and age
DG
Directed graphs
diagv
Matrix product with a diagonal matrix
drawGraph
Drawing a graph with a simple point and click interface.
dSep
d-separation
edgematrix
Edge matrix of a graph
essentialGraph
Essential graph
findPath
Finding paths
fitAncestralGraph
Fitting of Gaussian Ancestral Graph Models
fitConGraph
Fitting a Gaussian concentration graph model
fitCovGraph
Fitting of Gaussian covariance graph models
fitDag
Fitting of Gaussian DAG models
fitDagLatent
Fitting Gaussian DAG models with one latent variable
fitmlogit
Multivariate logistic models
fundCycles
Fundamental cycles
ggm
The package 'ggm': summary information
glucose
Glucose control
grMAT
Graph to adjacency matrix
icf
Iterative conditional fitting
In
Indicator matrix
InducedGraphs
Graphs induced by marginalization or conditioning
isAcyclic
Graph queries
isADMG
Acyclic directed mixed graphs
isAG
Ancestral graph
isGident
G-identifiability of an UG
MAG
Maximal ancestral graph
makeMG
Mixed Graphs
marg.param
Link function of marginal log-linear parameterization
MarkEqMag
Markov equivalence of maximal ancestral graphs
MarkEqRcg
Markov equivalence for regression chain graphs.
marks
Mathematics marks
mat.mlogit
Multivariate logistic parametrization
Max
Maximisation for graphs
MRG
Maximal ribbonless graph
msep
The m-separation criterion
MSG
Maximal summary graph
null
Null space of a matrix
parcor
Partial correlations
pcor
Partial correlation
pcor.test
Test for zero partial association
plotGraph
Plot of a mixed graph
powerset
Power set
rcorr
Random correlation matrix
RepMarBG
Representational Markov equivalence to bidirected graphs.
RepMarDAG
Representational Markov equivalence to directed acyclic...
RepMarUG
Representational Markov equivalence to undirected graphs.
RG
Ribbonless graph
rnormDag
Random sample from a decomposable Gaussian model
rsphere
Random vectors on a sphere
SG
summary graph
shipley.test
Test of all independencies implied by a given DAG
SimpleGraphOperations
Simple graph operations
stress
Stress
surdata
A simulated data set
swp
Sweep operator
topSort
Topological sort
transClos
Transitive closure of a graph
triDec
Triangular decomposition of a covariance matrix
UG
Defining an undirected graph (UG)
unmakeMG
Loopless mixed graphs components
UtilityFunctions
Utility functions

Files in this package

ggm
ggm/inst
ggm/inst/doc
ggm/inst/doc/mixed-graphs.pdf
ggm/NAMESPACE
ggm/NEWS
ggm/data
ggm/data/stress.rda
ggm/data/surdata.rda
ggm/data/glucose.rda
ggm/data/derived.rda
ggm/data/marks.rda
ggm/data/anger.rda
ggm/R
ggm/R/kayvan.R
ggm/R/functions.R
ggm/vignettes
ggm/vignettes/mixed-graphs.pdf
ggm/MD5
ggm/DESCRIPTION
ggm/man
ggm/man/powerset.Rd
ggm/man/stress.Rd
ggm/man/findPath.Rd
ggm/man/fitDag.Rd
ggm/man/derived.Rd
ggm/man/shipley.test.Rd
ggm/man/UtilityFunctions.Rd
ggm/man/MRG.Rd
ggm/man/Max.Rd
ggm/man/conComp.Rd
ggm/man/basiSet.Rd
ggm/man/fitDagLatent.Rd
ggm/man/blkdiag.Rd
ggm/man/icf.Rd
ggm/man/ggm.Rd
ggm/man/null.Rd
ggm/man/checkIdent.Rd
ggm/man/surdata.Rd
ggm/man/cycleMatrix.Rd
ggm/man/unmakeMG.Rd
ggm/man/isAcyclic.Rd
ggm/man/DG.Rd
ggm/man/adjMatrix.Rd
ggm/man/marg.param.Rd
ggm/man/mat.mlogit.Rd
ggm/man/MarkEqRcg.Rd
ggm/man/triDec.Rd
ggm/man/isGident.Rd
ggm/man/UG.Rd
ggm/man/dSep.Rd
ggm/man/DAG.Rd
ggm/man/pcor.Rd
ggm/man/fitCovGraph.Rd
ggm/man/RepMarBG.Rd
ggm/man/swp.Rd
ggm/man/drawGraph.Rd
ggm/man/isAG.Rd
ggm/man/makeMG.Rd
ggm/man/plotGraph.Rd
ggm/man/AG.Rd
ggm/man/MSG.Rd
ggm/man/anger.Rd
ggm/man/fitAncestralGraph.Rd
ggm/man/marks.Rd
ggm/man/glucose.Rd
ggm/man/blodiag.Rd
ggm/man/correlations.Rd
ggm/man/rcorr.Rd
ggm/man/fitConGraph.Rd
ggm/man/msep.Rd
ggm/man/essentialGraph.Rd
ggm/man/transClos.Rd
ggm/man/MAG.Rd
ggm/man/parcor.Rd
ggm/man/diagv.Rd
ggm/man/MarkEqMag.Rd
ggm/man/fitmlogit.Rd
ggm/man/In.Rd
ggm/man/RG.Rd
ggm/man/RepMarDAG.Rd
ggm/man/edgematrix.Rd
ggm/man/SG.Rd
ggm/man/topSort.Rd
ggm/man/grMAT.Rd
ggm/man/isADMG.Rd
ggm/man/rnormDag.Rd
ggm/man/SimpleGraphOperations.Rd
ggm/man/bfsearch.Rd
ggm/man/cmpGraph.Rd
ggm/man/InducedGraphs.Rd
ggm/man/pcor.test.Rd
ggm/man/RepMarUG.Rd
ggm/man/binve.Rd
ggm/man/allEdges.Rd
ggm/man/fundCycles.Rd
ggm/man/rsphere.Rd