FlowGraph               Construct FlowGraph object
L                       Get adjacency matrix for directed part.
MixedGraph              Construct MixedGraph object
MixedGraphFixedOrder    Construct MixedGraphFixedOrder object
O                       Get adjacency matrix for bidirected part.
SEMID-package           SEMID package documentation.
ancestors               All ancestors of a collection of nodes
ancestralID             Determines which edges in a mixed graph are
                        ancestralID-identifiable
ancestralIdentifyStep   Perform one iteration of ancestral
                        identification.
createAncestralIdentifier
                        Create an ancestral identification function.
createEdgewiseIdentifier
                        Create an edgewise identification function
createHalfTrekFlowGraph
                        Helper function to create a flow graph.
createHtcIdentifier     Create an htc identification function.
createHtrGraph          Helper function to create a graph encoding htr
                        relationships.
createIdentifierBaseCase
                        Create an identifier base case
createSimpleBiDirIdentifier
                        Identify bidirected edges if all directed edges
                        are identified
createTrGraph           Helper function to create a graph encoding trek
                        reachable relationships.
createTrekFlowGraph     Helper function to create a flow graph.
createTrekSeparationIdentifier
                        Create an trek separation identification
                        function
descendants             Get descendants of a node
edgewiseID              Determines which edges in a mixed graph are
                        edgewiseID-identifiable
edgewiseIdentifyStep    Perform one iteration of edgewise
                        identification.
edgewiseTSID            Determines which edges in a mixed graph are
                        edgewiseID+TS identifiable
flowBetween             Flow from one set of nodes to another.
generalGenericID        A general generic identification algorithm
                        template.
getAncestors            Get getAncestors of nodes in a graph.
getDescendants          Get descendants of nodes in a graph.
getHalfTrekSystem       Determines if a half-trek system exists in the
                        mixed graph.
getMaxFlow              Size of largest HT system Y satisfying the HTC
                        for a node v except perhaps having
                        |getParents(v)| < |Y|.
getMixedCompForNode     Get the mixed component of a node in a mixed
                        subgraph.
getParents              Get getParents of nodes in a graph.
getSiblings             Get getSiblings of nodes in a graph.
getTrekSystem           Determines if a trek system exists in the mixed
                        graph.
graphID                 Identifiability of linear structural equation
                        models.
graphID.ancestralID     Determine generic identifiability of an acyclic
                        mixed graph using ancestral decomposition.
graphID.decompose       Determine generic identifiability by Tian
                        Decomposition and HTC
graphID.genericID       Determine generic identifiability of a mixed
                        graph.
graphID.globalID        Check for global identifiability of a mixed
                        graph.
graphID.htcID           Determines if a mixed graph is
                        HTC-identifiable.
graphID.main            Helper function to handle a graph component.
graphID.nonHtcID        Check for generic infinite-to-one via the
                        half-trek criterion.
htcID                   Determines which edges in a mixed graph are
                        HTC-identifiable.
htcIdentifyStep         Perform one iteration of HTC identification.
htr                     Get all HTR nodes from a set of nodes in a
                        graph.
htrFrom                 Half trek reachable nodes.
inducedSubgraph         Get the induced subgraph on a collection of
                        nodes
isSibling               Are two nodes siblings?
mixedGraphHasSimpleNumbering
                        Checks a MixedGraph has appropriate node
                        numbering
nodes                   Get all nodes in the graph.
numNodes                Number of nodes in the graph.
parents                 All parents a collection of nodes.
plot.MixedGraph         Plots the mixed graph
plotMixedGraph          Plot a mixed graph
print.GenericIDResult   Prints a GenericIDResult object
print.SEMIDResult       Prints a SEMIDResult object
semID                   Identifiability of linear structural equation
                        models.
siblings                All siblings of a collection of nodes
stronglyConnectedComponent
                        Strongly connected component
stronglyConnectedComponents
                        Strongly connected components
subsetsOfSize           Returns all subsets of a certain size
tianComponent           Returns the Tian c-component of a node
tianDecompose           Performs the tian decomposition on the mixed
                        graph
tianIdentifier          Identifies components in a tian decomposition
tianSigmaForComponent   Globally identify the covariance matrix of a
                        C-component
toEx                    Transforms a vector of node indices in the
                        internal rep. into external numbering
toIn                    Transforms a vector of given node indices into
                        their internal numbering
trFrom                  Trek reachable nodes.
trekSeparationIdentifyStep
                        Perform one iteration of trek separation
                        identification.
updateEdgeCapacities    Update edge capacities.
updateVertexCapacities
                        Update vertex capacities.
validateMatrices        A helper function to validate input matrices.
