R Observatory: Metrics for hdmed version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-11-28. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.0.1, its last release before removal.

hdmed

1.0.1

Methods for Mediation Analysis with High-Dimensional Mediators

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Dylan Clark-Boucher2 releasesCRAN page ↗

A suite of functions for performing mediation analysis with high-dimensional mediators. In addition to centralizing code from several existing packages for high-dimensional mediation analysis, we provide organized, well-documented functions for a handle of methods which, though programmed their original authors, have not previously been formalized into R packages or been made presentable for public use. The methods we include cover a broad array of approaches and objectives, and are described in detail by both our companion manuscript---"Methods for Mediation Analysis with High-Dimensional DNA Methylation Data: Possible Choices and Comparison"---and the original publications that proposed them. The specific methods offered by our package include the Bayesian sparse linear mixed model (BSLMM) by Song et al. (2019); high-dimensional mediation analysis (HDMA) by Gao et al. (2019); high-dimensional multivariate mediation (HDMM) by Chén et al. (2018); high-dimensional linear mediation analysis (HILMA) by Zhou et al. (2020); high-dimensional mediation analysis (HIMA) by Zhang et al. (2016); latent variable mediation analysis (LVMA) by Derkach et al. (2019); mediation by fixed-effect model (MedFix) by Zhang (2021); pathway LASSO by Zhao & Luo (2022); principal component mediation analysis (PCMA) by Huang & Pan (2016); and sparse principal component mediation analysis (SPCMA) by Zhao et al. (2020). Citations for the corresponding papers can be found in their respective functions.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/hdmed/hdmed_1.0.1.tar.gz"
pkgFile <- "hdmed_1.0.1.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 (1.0.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-hdmed

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-hdmed

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

12

Dependencies · direct

Documentation

READMEYes · 1,022 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 91%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on75 r2u15 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (12)

bama foreach freebird gcdnet genlasso hdi iterators (>= 1.0.14)MASSmediation ncvregstatsutils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Dylan Clark-Boucher

Author, Maintainer

Authors (2)

Dylan Clark-Boucher

Author, Maintainer

Mike Kleinsasser

Author

Package Timeline

2 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
2025-11-28
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
1.0.1
2024-05-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.0
2023-02-27
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 2
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 17 KB / 1 file
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("hdmed")

Format

Clark-Boucher, D., & Kleinsasser, M. (n.d.). hdmed: Methods for Mediation Analysis with High-Dimensional Mediators (Version 1.0.1) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=hdmed

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 hdmed version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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