ggm: Functions for graphical Markov models

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

AuthorGiovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Date of publication2015-01-21 12:47:19
MaintainerGiovanni M. Marchetti <giovanni.marchetti@disia.unifi.it>
LicenseGPL (>= 2)
Version2.3

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

Functions

adjMatrix Man page
AG Man page
allEdges Man page
anger Man page
basiSet Man page
bd Man page
bfsearch Man page
binve Man page
blkdiag Man page
blodiag Man page
ch Man page
checkIdent Man page
cmpGraph Man page
conComp Man page
correlations Man page
cycleMatrix Man page
DAG Man page
derived Man page
DG Man page
diagv Man page
drawGraph Man page
dSep Man page
edgematrix Man page
essentialGraph Man page
findPath Man page
fitAncestralGraph Man page
fitConGraph Man page
fitCovGraph Man page
fitDag Man page
fitDagLatent Man page
fitmlogit Man page
fundCycles Man page
ggm Man page
glucose Man page
grMAT Man page
icf Man page
icfmag Man page
In Man page
inducedChainGraph Man page
inducedConGraph Man page
inducedCovGraph Man page
inducedDAG Man page
InducedGraphs Man page
inducedRegGraph Man page
isAcyclic Man page
isADMG Man page
isAG Man page
isGident Man page
likGau Man page
MAG Man page
makeMG Man page
marg.param Man page
MarkEqMag Man page
MarkEqRcg Man page
marks Man page
mat.mlogit Man page
Max Man page
MRG Man page
msep Man page
MSG Man page
null Man page
pa Man page
parcor Man page
pcor Man page
pcor.test Man page
plotGraph Man page
powerset Man page
rcorr Man page
rem Man page
RepMarBG Man page
RepMarDAG Man page
RepMarUG Man page
RG Man page
rnormDag Man page
RR Man page
rsphere Man page
SG Man page
shipley.test Man page
SPl Man page
stress Man page
surdata Man page
swp Man page
topOrder Man page
topSort Man page
transClos Man page
triDec Man page
UG Man page
unmakeMG Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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