R Observatory: Metrics for HEMDAG version 2.7.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 2.7.4, its last release before removal.

HEMDAG

2.7.4Package record

Hierarchical Ensemble Methods for Directed Acyclic Graphs

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Marco NotaroCRAN page ↗GitHub ↗Website ↗

An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) doi:10.1186/s12859-017-1854-y).

Changes in 2.7.4

Changes

remove extra input parameter `f.criterion from tpr.dag.cv, tpr.dag.holdout, find.best.f and compute.fmax: type of F-measure used to select the best F-measure is always the harmonic mean between the average precision and recall (f.criterion="F") and never the F-measure computed as average across examples (f.criterion="avF"`);
fix a minor bug in `tpr.dag.holdout`;
add warning checks in `tpr.dag.cv and tpr.dag.holdout`;
improve some test cases and manual;

From NEWS.md in the release

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/HEMDAG/HEMDAG_2.7.4.tar.gz"
pkgFile <- "HEMDAG_2.7.4.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (2.7.4) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("marconotaro/hemdag")

Development version from marconotaro/hemdag. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.7.4

READMENoVignettesNoNEWSYes · 100% structured · mentions 2.7.4Citation fileYes · cites a publicationWebsiteYes

Help pages: 56includes a package overview page
Examples that run: 98%53 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 2%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on324 r2u3.1K bioconda

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (9)

graph RBGL precrec preprocessCoremethodsplyr foreach doParallelparallel

LinkingTo (0)

none

Suggests (2)

Rgraphviz testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Marco Notaro

Author, Maintainer since 1.0.0 (2017)

Giorgio Valentini

Author

Alessandro Petrini

Contributor · added in 2.2.3

Releases (17)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.7.4
record
2021-02-12 · diff ↗
2.7.3
record
2020-09-19 · diff ↗ ·
removed 35 exports
AUPRC.single.class, AUPRC.single.over.classes, AUROC.single.class, AUROC.single.over.classes, Do.GPAV, Do.GPAV.holdout, Do.HTD, Do.HTD.holdout, Do.TPR.DAG, Do.TPR.DAG.holdout, Do.flat.scores.normalization, Do.full.annotation.matrix, Do.heuristic.methods, Do.heuristic.methods.holdout, GPAV, GPAV.over.examples, GPAV.parallel, TPR.DAG, check.DAG.integrity, compute.Fmeasure.multilabel, do.edges.from.HPO.obo, do.stratified.cv.data.over.classes, do.stratified.cv.data.single.class, do.subgraph, do.submatrix, do.unstratified.cv.data, get.children.bottom.up, get.children.top.down, get.parents, get.parents.bottom.up and 5 more

added 35 exports
auprc.single.class, auprc.single.over.classes, auroc.single.class, auroc.single.over.classes, build.children.bottom.up, build.children.top.down, build.edges.from.hpo.obo, build.parents, build.parents.bottom.up, build.parents.top.down, build.parents.topological.sorting, build.scores.matrix.from.list, build.scores.matrix.from.tupla, build.subgraph, build.submatrix, check.dag.integrity, compute.fmax, gpav, gpav.holdout, gpav.over.examples, gpav.parallel, gpav.vanilla, htd.holdout, htd.vanilla, obozinski.and, obozinski.holdout, obozinski.max, obozinski.methods, obozinski.or, stratified.cv.data.over.classes and 5 more
R
R 4.0.0 released · 2020-04-24
2.6.1
record
2020-03-03 · diff ↗
2.6.0
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2019-11-15 · diff ↗
2.5.9
record
2019-10-08 · diff ↗ ·
removed 12 exports
descens.tau, descens.threshold, descens.threshold.free, descens.weighted.threshold, descens.weighted.threshold.free, heuristicAND, heuristicMAX, heuristicOR, tpr.threshold, tpr.threshold.free, tpr.weighted.threshold, tpr.weighted.threshold.free

added 4 exports
build.consistent.graph, heuristic.and, heuristic.max, heuristic.or
2.4.8
record
2019-05-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.4.7
record
2019-03-18 · diff ↗

Show 12 earlier eventsHide 12 earlier events

2.3.6
record
2019-03-09 · diff ↗ ·
added 1 export
lexicographical.topological.sort
2.2.5
record
2018-09-21 · diff ↗ ·
removed 1 export
PXR.at.multiple.recall.levels.over.classes

added 3 exports
create.stratified.fold.df, precision.at.all.recall.levels.single.class, precision.at.given.recall.levels.over.classes
2.2.4
record
2018-08-18 · diff ↗
2.2.3
record
2018-08-15 · diff ↗ ·
added 6 exports
Do.GPAV, Do.GPAV.holdout, GPAV, GPAV.over.examples, GPAV.parallel, adj.upper.tri
2.1.3
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2018-05-21 · diff ↗
2.1.2
record
2018-05-07 · diff ↗ ·
removed 1 export
Do.FLAT.scores.normalization

added 4 exports
Do.flat.scores.normalization, PXR.at.multiple.recall.levels.over.classes, compute.Fmeasure.multilabel, scores.normalization
R
R 3.5.0 released · 2018-04-23
2.0.1
record
2018-02-02 · diff ↗
2.0.0
record
2018-01-23 · diff ↗ ·
removed 18 exports
Do.descens.tau.cv, Do.descens.tau.holdout, Do.descens.threshold.cv, Do.descens.threshold.free, Do.descens.threshold.free.holdout, Do.descens.threshold.holdout, Do.descens.weighted.threshold.cv, Do.descens.weighted.threshold.free.cv, Do.descens.weighted.threshold.free.holdout, Do.descens.weighted.threshold.holdout, Do.tpr.threshold.cv, Do.tpr.threshold.free, Do.tpr.threshold.free.holdout, Do.tpr.threshold.holdout, Do.tpr.weighted.threshold.cv, Do.tpr.weighted.threshold.free.cv, Do.tpr.weighted.threshold.free.holdout, Do.tpr.weighted.threshold.holdout

added 3 exports
Do.TPR.DAG, Do.TPR.DAG.holdout, TPR.DAG
1.1.1
record
2017-10-16 · diff ↗ ·
added 21 exports
Do.descens.tau.cv, Do.descens.tau.holdout, Do.descens.threshold.cv, Do.descens.threshold.free, Do.descens.threshold.free.holdout, Do.descens.threshold.holdout, Do.descens.weighted.threshold.cv, Do.descens.weighted.threshold.free.cv, Do.descens.weighted.threshold.free.holdout, Do.descens.weighted.threshold.holdout, Do.heuristic.methods, Do.heuristic.methods.holdout, descens.tau, descens.threshold, descens.threshold.free, descens.weighted.threshold, descens.weighted.threshold.free, heuristicAND, heuristicMAX, heuristicOR, tupla.matrix
1.0.0
record
2017-08-11
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-11
Total releases: 17 / 9 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 26 KB / 5 files

Cite

Cite this package

Run in R for the authors' entry:

citation("HEMDAG")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1186/s12859-017-1854-y.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for HEMDAG version 2.7.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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