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| HEMDAG-package | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs |
| 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 |
| build.ancestors | Build ancestors |
| build.ancestors.bottom.up | Build ancestors |
| build.ancestors.per.level | Build ancestors |
| build.children | Build children |
| build.consistent.graph | Build Consistent Graph |
| build.descendants | Build descendants |
| build.descendants.bottom.up | Build descendants |
| build.descendants.per.level | Build descendants |
| check.annotation.matrix.integrity | Annotation matrix checker |
| check.DAG.integrity | DAG checker |
| check.hierarchy | Hierarchical constraints checker |
| check.hierarchy.single.sample | Hierarchical constraints checker |
| children | Build children |
| compute.flipped.graph | Flip Graph |
| compute.Fmeasure.multilabel | Compute F-measure Multilabel |
| constraints.matrix | Constraints Matrix |
| create.stratified.fold.df | DataFrame for Stratified Cross Validation |
| descendants | Build descendants |
| 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 annotation 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 |
| 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 |
| FMM | Compute F-measure Multilabel |
| full.annotation.matrix | Full annotation matrix |
| 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 |
| HEMDAG | HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs |
| Heuristic-Methods | Obozinski Heuristic Methods |
| heuristic.and | Obozinski Heuristic Methods |
| heuristic.max | Obozinski Heuristic Methods |
| heuristic.or | Obozinski Heuristic Methods |
| hierarchical.checkers | Hierarchical constraints checker |
| htd | HTD-DAG |
| HTD-DAG | HTD-DAG |
| L | Small real example datasets |
| lexicographical.topological.sort | Lexicographical Topological Sorting |
| Multilabel.F.measure | Multilabel F-measure |
| normalize.max | Max normalization |
| 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 |
| 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 |
| 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 |
| transitive.closure.annotations | Transitive closure of annotations |
| tupla.matrix | Tupla Matrix |
| W | Small real example datasets |
| weighted.adjacency.matrix | Weighted Adjacency Matrix |
| write.graph | Write a directed graph on file |