# Hierarchical Ensemble Methods for Directed Acyclic Graphs

## Documentation for package ‘HEMDAG’ version 2.7.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

HEMDAG-package | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs
adj.upper.tri | Binary upper triangular adjacency matrix
auprc | AUPRC measures
auprc.single.class | AUPRC measures
auprc.single.over.classes | AUPRC measures
auroc | AUROC measures
auroc.single.class | AUROC measures
auroc.single.over.classes | AUROC measures
build.ancestors | Build ancestors
build.ancestors.bottom.up | Build ancestors
build.ancestors.per.level | Build ancestors
build.children | Build children
build.children.bottom.up | Build children
build.children.top.down | Build children
build.consistent.graph | Build consistent graph
build.descendants | Build descendants
build.descendants.bottom.up | Build descendants
build.descendants.per.level | Build descendants
build.edges.from.hpo.obo | Parse an HPO obo file
build.parents | Build parents
build.parents.bottom.up | Build parents
build.parents.top.down | Build parents
build.parents.topological.sorting | Build parents
build.scores.matrix | Build scores matrix
build.scores.matrix.from.list | Build scores matrix
build.scores.matrix.from.tupla | Build scores matrix
build.subgraph | Build subgraph
build.submatrix | Build submatrix
check.annotation.matrix.integrity | Annotation matrix checker
check.dag.integrity | DAG checker
check.hierarchy | Hierarchical constraints checker
check.hierarchy.single.sample | Hierarchical constraints checker
compute.flipped.graph | Flip graph
compute.fmax | Compute Fmax
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
F.measure.multilabel | multilabel F-measure
F.measure.multilabel-method | multilabel F-measure
find.best.f | Best hierarchical F-score
find.leaves | Leaves
fmax | Compute Fmax
full.annotation.matrix | Full annotation matrix
g | Small real example datasets
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
HEMDAG | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs
hierarchical.checkers | Hierarchical constraints checker
htd | HTD-DAG
htd.holdout | HTD-DAG holdout
htd.vanilla | HTD-DAG vanilla
L | Small real example datasets
lexicographical.topological.sort | Lexicographical topological sorting
multilabel.F.measure | multilabel F-measure
normalize.max | Max normalization
obozinski.and | Obozinski heuristic methods
obozinski.heuristic.methods | Obozinski heuristic methods
obozinski.holdout | Obozinski's heuristic methods - holdout
obozinski.max | Obozinski heuristic methods
obozinski.methods | Obozinski's heuristic methods calling
obozinski.or | Obozinski heuristic methods
precision.at.all.recall.levels.single.class | Precision-Recall curves
precision.at.given.recall.levels.over.classes | Precision-Recall curves
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
S | Small real example datasets
scores.normalization | Scores normalization function
specific.annotation.list | Specific annotations list
specific.annotation.matrix | Specific annotation matrix
stratified.cross.validation | Stratified cross validation
stratified.cv.data.over.classes | Stratified cross validation
stratified.cv.data.single.class | Stratified cross validation
test.index | Small real example datasets
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
W | Small real example datasets
weighted.adjacency.matrix | Weighted adjacency matrix
write.graph | Write a directed graph on file