# Hierarchical Ensemble Methods for Directed Acyclic Graphs

## Documentation for package ‘HEMDAG’ version 2.4.7

- DESCRIPTION file.

## Help Pages

A B C D E F G H L M N P R S T W

HEMDAG-package | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

## -- A --

adj.upper.tri | Binary Upper Triangular Adjacency Matrix
ancestors | Build ancestors
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

## -- B --

build.ancestors | Build ancestors
build.ancestors.bottom.up | Build ancestors
build.ancestors.per.level | Build ancestors
build.children | Build children
build.descendants | Build descendants
build.descendants.bottom.up | Build descendants
build.descendants.per.level | Build descendants

## -- C --

check.annotation.matrix.integrity | Annotation matrix checker
check.DAG.integrity | DAG checker
check.hierarchy | Hierarchical constraints cheker
check.hierarchy.single.sample | Hierarchical constraints cheker
children | Build children
compute.flipped.graph | Flip Graph
compute.Fmeasure.multilabel | Compute Multilabel F-measure
constraints.matrix | Constraints Matrix
create.stratified.fold.df | DataFrame for Stratified Cross Validation

## -- D --

descendants | Build descendants
descens.tau | Defunct functions in package 'HEMDAG'.
descens.threshold | Defunct functions in package 'HEMDAG'.
descens.threshold.free | Defunct functions in package 'HEMDAG'.
descens.weighted.threshold | Defunct functions in package 'HEMDAG'.
descens.weighted.threshold.free | Defunct functions in package 'HEMDAG'.
distances.from.leaves | Distances from leaves
do.edges.from.HPO.obo | Parse an HPO OBO file
Do.flat.scores.normalization | Flat scores normalization
Do.full.annotation.matrix | Do full annotations matrix
Do.GPAV | GPAV - High Level Function
Do.GPAV.holdout | GPAV holdout
Do.heuristic.methods | Do Heuristic Methods
Do.heuristic.methods.holdout | Do Heuristic Methods holdout
Do.HTD | HTD-DAG vanilla
Do.HTD.holdout | HTD-DAG holdout
do.stratified.cv.data.over.classes | Stratified Cross Validation
do.stratified.cv.data.single.class | Stratified Cross Validation
do.subgraph | Build subgraph
do.submatrix | Build submatrix
Do.TPR.DAG | TPR-DAG cross-validation experiments
Do.TPR.DAG.holdout | TPR-DAG holdout experiments
do.unstratified.cv.data | Unstratified Cross Validation

## -- E --

example.datasets | Small real example datasets

## -- F --

F.measure.multilabel | Multilabel F-measure
F.measure.multilabel-method | Multilabel F-measure
find.best.f | Best hierarchical F-score
find.leaves | Leaves
FMM | Compute Multilabel F-measure
full.annotation.matrix | Full annotations matrix

## -- G --

g | Small real example datasets
get.children.bottom.up | Build children
get.children.top.down | Build children
get.parents | Build parents
get.parents.bottom.up | Build parents
get.parents.top.down | Build parents
get.parents.topological.sorting | Build parents
GPAV | Generalized Pool-Adjacent Violators
GPAV.over.examples | GPAV Over Examples
GPAV.parallel | GPAV Over Examples - Parallel Implementation
graph.levels | Build Graph Levels

## -- H --

HEMDAG | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs
HEMDAG-defunct | Defunct functions in package 'HEMDAG'.
Heuristic-Methods | Obozinski Heuristic Methods
heuristicAND | Obozinski Heuristic Methods
heuristicMAX | Obozinski Heuristic Methods
heuristicOR | Obozinski Heuristic Methods
hierarchical.checkers | Hierarchical constraints cheker
htd | HTD-DAG
HTD-DAG | HTD-DAG

## -- L --

L | Small real example datasets
lexicographical.topological.sort | Lexicographical Topological Sorting

## -- M --

Multilabel.F.measure | Multilabel F-measure

## -- N --

normalize.max | Max normalization

## -- P --

parents | Build parents
precision.at.all.recall.levels.single.class | Precision-Recall Measure
precision.at.given.recall.levels.over.classes | Precision-Recall Measure
PXR | Precision-Recall Measure

## -- R --

read.graph | Read a directed graph from a file
read.undirected.graph | Read an undirected graph from a file
root.node | Root node

## -- S --

S | Small real example datasets
scores.normalization | Scores Normalization Function
specific.annotation.list | Specific annotations list
specific.annotation.matrix | HPO specific annotations matrix
stratified.cross.validation | Stratified Cross Validation

## -- T --

test.index | Small real example datasets
TPR-DAG-cross-validation | TPR-DAG cross-validation experiments
TPR-DAG-holdout | TPR-DAG holdout experiments
TPR-DAG-variants | TPR-DAG Ensemble Variants
TPR.DAG | TPR-DAG Ensemble Variants
tpr.threshold | Defunct functions in package 'HEMDAG'.
tpr.threshold.free | Defunct functions in package 'HEMDAG'.
tpr.weighted.threshold | Defunct functions in package 'HEMDAG'.
tpr.weighted.threshold.free | Defunct functions in package 'HEMDAG'.
transitive.closure.annotations | Transitive closure of annotations
tupla.matrix | Tupla Matrix

## -- W --

W | Small real example datasets
weighted.adjacency.matrix | Weighted Adjacency Matrix
write.graph | Write a directed graph on file