hdmed: Methods for Mediation Analysis with High-Dimensional Mediators
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.
| Version: |
1.0.1 |
| Depends: |
R (≥ 2.10) |
| Imports: |
bama (≥ 1.3.0), foreach (≥ 1.5.2), freebird (≥ 1.0), gcdnet (≥ 1.0.6), genlasso (≥ 1.6.1), hdi (≥ 0.1.9), iterators (≥
1.0.14), MASS, mediation (≥ 4.5.0), ncvreg (≥ 3.13.0), stats, utils |
| Published: |
2024-05-15 |
| DOI: |
10.32614/CRAN.package.hdmed |
| Author: |
Dylan Clark-Boucher [aut, cre],
Mike Kleinsasser [aut] |
| Maintainer: |
Dylan Clark-Boucher <dclarkboucher at fas.harvard.edu> |
| License: |
GPL (≥ 3) |
| NeedsCompilation: |
no |
| Citation: |
hdmed citation info |
| Materials: |
README |
| CRAN checks: |
hdmed results [issues need fixing before 2025-11-15] |
Documentation:
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