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 |