# Graphical Markov Models with Mixed Graphs

## Documentation for package ‘ggm’ version 2.5

- DESCRIPTION file.
- Package NEWS.

## Help 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
bd | Simple graph operations
bfsearch | Breadth first search
binve | Inverts a marginal log-linear parametrization
blkdiag | Block diagonal matrix
blodiag | Block diagonal matrix
ch | Simple graph operations
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
In | Indicator matrix
inducedChainGraph | Graphs induced by marginalization or conditioning
inducedConGraph | Graphs induced by marginalization or conditioning
inducedCovGraph | Graphs induced by marginalization or conditioning
inducedDAG | Graphs induced by marginalization or conditioning
InducedGraphs | Graphs induced by marginalization or conditioning
inducedRegGraph | Graphs induced by marginalization or conditioning
isAcyclic | Graph queries
isADMG | Acyclic directed mixed graphs
isAG | Ancestral graph
isGident | G-identifiability of an UG
likGau | Utility functions
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
pa | Simple graph operations
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
rem | Utility functions
RepMarBG | Representational Markov equivalence to bidirected graphs.
RepMarDAG | Representational Markov equivalence to directed acyclic graphs.
RepMarUG | Representational Markov equivalence to undirected graphs.
RG | Ribbonless graph
rnormDag | Random sample from a decomposable Gaussian model
RR | Utility functions
rsphere | Random vectors on a sphere
SG | summary graph
shipley.test | Test of all independencies implied by a given DAG
SPl | Utility functions
stress | Stress
surdata | A simulated data set
swp | Sweep operator
topOrder | Topological sort
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