R Observatory: Metrics for HDMT version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HDMT

1.0.5Package record

A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses

3packages depend

5.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by James DaiCRAN page ↗

A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge. Methods used in the package refer to James Y. Dai, Janet L. Stanford & Michael LeBlanc (2020) doi:10.1080/01621459.2020.1765785.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("HDMT", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-hdmt

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-HDMT

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-15
ERROR12 OK, 1 ERROR2026-09-25
OK13 OK2026-09-18
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-31

Show 39 earlier changesHide 39 earlier changes

ERROR12 OK, 1 ERROR2026-08-27
OK13 OK2026-08-25
ERROR12 OK, 1 ERROR2026-08-20
OK13 OK2026-08-12
ERROR12 OK, 1 ERROR2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-07-21
ERROR12 OK, 1 ERROR2026-07-18
OK13 OK2026-07-13
ERROR12 OK, 1 ERROR2026-07-11
OK13 OK2026-07-07
ERROR12 OK, 1 ERROR2026-07-04
OK13 OK2026-06-30
ERROR12 OK, 1 ERROR2026-06-29
OK13 OK2026-06-22
ERROR12 OK, 1 ERROR2026-06-20
OK13 OK2026-06-15
ERROR12 OK, 1 ERROR2026-06-13
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-06
OK13 OK2026-06-05
ERROR12 OK, 1 ERROR2026-06-01
OK13 OK2026-05-27
ERROR12 OK, 1 ERROR2026-05-24
OK13 OK2026-05-14
ERROR12 OK, 1 ERROR2026-05-11
OK13 OK2026-05-06
ERROR12 OK, 1 ERROR2026-05-04
OK14 OK2026-04-24
ERROR13 OK, 1 ERROR2026-04-22
OK14 OK2026-04-16
ERROR13 OK, 1 ERROR2026-04-15
OK14 OK2026-04-09
ERROR13 OK, 1 ERROR2026-04-07
OK14 OK2026-04-02
ERROR13 OK, 1 ERROR2026-03-21
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 100%

Vignettes (1)

HDMT HTML

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #5,250 · ~16/day · ~479/mo

Releases R versions

Daily download trend is not available in this view yet.

61230 days

1.6K90 days

5.7K1 year

Compare downloads with other packages →

Also on107 r2u9 autocran112 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing HDMT adds 1 package (1 with compiled code, 59 KB of source tarballs). Heaviest: fdrtool 59 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.4.0

Imports (2)

fdrtool qvalue

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

HIMA medScan TransHDM

How these are counted

Code & Tests

Datasets

People & History

People (2)

James Dai

Author, Maintainer since 1.0 (2019)

Xiaoyu Wang

Author

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
1.0.5Latest
record
2022-01-29 · current release · diff ↗
1.0.4
record
2021-12-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.3
record
2021-02-20 · diff ↗
1.0.2
record
2020-10-07 · diff ↗ ·
removed 3 exports
nullestimation, fwerest, fdrest

added 3 exports
null_estimation, fwer_est, fdr_est
R
R 4.0.0 released · 2020-04-24
1.0.1
record
2019-12-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0
record
2019-04-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-16
Total releases: 6 / 7 yrs
License: MIT + file LICENSE OSI · relicensed from GPL (>= 2) in 1.0.5
Minimum R: ≥ 3.4.0
Bundled data: 1.7 MB / 3 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HDMT")

Format

Dai, J., & Wang, X. (2022). HDMT: A Multiple Testing Procedure for High-Dimensional Mediation Hypotheses (Version 1.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.HDMT

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 HDMT version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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