Hierarchical Ensemble Methods for Directed Acyclic Graphs
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Documentation for package ‘HEMDAG’ version 2.7.4
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| 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 |