F1                      F1 score
FDR                     False Discovery Rate
FOR                     False Omission Rate
G1                      G1 score
NPV                     Negative predictive value
TemporalBDeu-class      Temporal Bayesian Dirichlet equivalent uniform
                        (Score criterion)
TemporalBIC-class       Temporal Bayesian Information Criterion (Score
                        criterion)
adj_confusion           Compute confusion matrix for comparing two
                        adjacency matrices
amat                    Extract adjacency matrix from tpdag, cpdag,
                        tpag or pag object
as.graphNEL             Convert adjacency matrix to graphNEL object
average_degree          Compute average degree for adjacency matrix
compare                 Compare two tpdag or tskeleton objects
confusion               Compute confusion matrix for comparing two
                        adjacency matrices
corTest                 Test for vanishing partial correlations
dir_confusion           Compute confusion matrix for comparing two
                        adjacency matrices
dir_confusion_original
                        Compute confusion matrix for comparing two
                        adjacency matrices
edges                   List of edges in adjacency matrix
essgraph2amat           Convert essential graph to adjacency matrix
evaluate                Evaluate adjacency matrix estimation
evaluate.array          Evaluate adjacency matrix estimation
evaluate.matrix         Evaluate adjacency matrix estimation
evaluate.tamat          Evaluate adjacency matrix estimation
fci                     Perform causal discovery using the FCI
                        algorithm
gausCorScore            Gaussian L0 score computed on correlation
                        matrix
getvar.character        Get variables with a specific prefix (character
                        method)
getvar.data.frame       Get variables with a specific prefix
                        (data.frame method)
graph2amat              Convert graphNEL object to adjacency matrix
is_cpdag                Check for CPDAG
is_pdag                 Check for PDAG
maketikz                Generate Latex tikz code for plotting a
                        temporal DAG, PDAG or PAG.
maxnedges               Compute maximal number of edges for graph
nDAGs                   Number of different DAGs
nedges                  Number of edges in adjacency matrix
pc                      Perform causal discovery using the PC algorithm
plot.pag                Plot partial ancestral graph (PAG)
plot.tamat              Plot adjacency matrix with order information
plot.tpag               Plot temporal partial ancestral graph (TPAG)
plot.tpdag              Plot temporal partially directed acyclic graph
                        (TPDAG)
plot.tskeleton          Plot temporal skeleton
plotTempoMech           Plot temporal data generating mechanism
precision               Precision
probmat2amat            Convert a matrix of probabilities into an
                        adjacency matrix
recall                  Recall
regTest                 Regression-based information loss test
shd                     Structural hamming distance between adjacency
                        matrices
simDAG                  Simulate a random DAG
simGausFromDAG          Simulate Gaussian data according to DAG
specificity             Specificity
tamat                   Make a temporal adjacency matrix
tfci                    Perform causal discovery using the temporal FCI
                        algorithm (TFCI)
tges                    Estimate the restricted Markov equivalence
                        class using Temporal Greedy Equivalence Search
tpc                     Perform causal discovery using the temporal PC
                        algorithm (TPC)
tpcExample              Simulated data example
tplot                   Plot temporal graph via Latex
