HEMDAG-package          HEMDAG: Hierarchical Ensemble Methods for
                        Directed Acyclic Graphs
adj.upper.tri           Binary upper triangular adjacency matrix
auprc                   AUPRC measures
auroc                   AUROC measures
build.ancestors         Build ancestors
build.children          Build children
build.consistent.graph
                        Build consistent graph
build.descendants       Build descendants
build.edges.from.hpo.obo
                        Parse an HPO obo file
build.parents           Build parents
build.scores.matrix     Build scores matrix
build.subgraph          Build subgraph
build.submatrix         Build submatrix
check.annotation.matrix.integrity
                        Annotation matrix checker
check.dag.integrity     DAG checker
compute.flipped.graph   Flip graph
constraints.matrix      Constraints matrix
create.stratified.fold.df
                        DataFrame for stratified cross validation
distances.from.leaves   Distances from leaves
example.datasets        Small real example datasets
find.best.f             Best hierarchical F-score
find.leaves             Leaves
fmax                    Compute Fmax
full.annotation.matrix
                        Full annotation matrix
gpav                    Generalized Pool-Adjacent Violators (GPAV)
gpav.holdout            GPAV holdout
gpav.over.examples      GPAV over examples
gpav.parallel           GPAV over examples - parallel implementation
gpav.vanilla            GPAV vanilla
graph.levels            Build graph levels
hierarchical.checkers   Hierarchical constraints checker
htd                     HTD-DAG
htd.holdout             HTD-DAG holdout
htd.vanilla             HTD-DAG vanilla
lexicographical.topological.sort
                        Lexicographical topological sorting
multilabel.F.measure    multilabel F-measure
normalize.max           Max normalization
obozinski.heuristic.methods
                        Obozinski heuristic methods
obozinski.holdout       Obozinski's heuristic methods - holdout
obozinski.methods       Obozinski's heuristic methods calling
pxr                     Precision-Recall curves
read.graph              Read a directed graph from a file
read.undirected.graph   Read an undirected graph from a file
root.node               Root node
scores.normalization    Scores normalization function
specific.annotation.list
                        Specific annotations list
specific.annotation.matrix
                        Specific annotation matrix
stratified.cross.validation
                        Stratified cross validation
tpr.dag                 TPR-DAG ensemble variants
tpr.dag.cv              TPR-DAG cross-validation experiments
tpr.dag.holdout         TPR-DAG holdout experiments
transitive.closure.annotations
                        Transitive closure of annotations
tupla.matrix            Tupla matrix
unstratified.cv.data    Unstratified cross validation
weighted.adjacency.matrix
                        Weighted adjacency matrix
write.graph             Write a directed graph on file
