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

2.7.4

Hierarchical Ensemble Methods for Directed Acyclic Graphs

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Marco Notaro17 releasesCRAN page ↗GitHub ↗

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).

Install

R (source archive)pak (dev)Ubuntu (r2u)

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.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hemdag

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.48

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 99%
Return-value docs: 100%
References docs: 2%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on363 r2u3K bioconda

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.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Marco Notaro

Author, Maintainer

Authors (2)

Marco Notaro

Author, Maintainer

Giorgio Valentini

Author · added in 2.2.3

Contributors (1)

Alessandro Petrini

Contributor · added in 2.2.3

Listed in earlier versions (3)

Giorgio Valentini (AnacletoLab

no longer listed · 1.0.0 to 2.1.3

Dipartimento di Informatica

no longer listed · 1.0.0 to 2.1.3

Universita' degli Studi di Milano)

no longer listed · 1.0.0 to 2.1.3

Package Timeline

17 releases. Pick two to compare their code metrics. R releases are shown for context.

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
2021-02-12 · diff ↗
2.7.3
2020-09-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.6.1
2020-03-03 · diff ↗
2.6.0
2019-11-15 · diff ↗
2.5.9
2019-10-08 · diff ↗
2.4.8
2019-05-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.4.7
2019-03-18 · diff ↗

Show 12 earlier events

2.3.6
2019-03-09 · diff ↗
2.2.5
2018-09-21 · diff ↗
2.2.4
2018-08-18 · diff ↗
2.2.3
2018-08-15 · diff ↗
2.1.3
2018-05-21 · diff ↗
2.1.2
2018-05-07 · diff ↗
R
R 3.5.0 released · 2018-04-23
2.0.1
2018-02-02 · diff ↗
2.0.0
2018-01-23 · diff ↗
1.1.1
2017-10-16 · diff ↗
1.0.0
2017-08-11
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 17
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 26 KB / 5 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HEMDAG")

Format

Notaro, M., Petrini, A., & Valentini, G. (n.d.). HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs (Version 2.7.4) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=HEMDAG

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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