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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 |
| Reference manual: | hdmed.pdf |
| Package source: | hdmed_1.0.1.tar.gz |
| Windows binaries: | r-devel: hdmed_1.0.1.zip, r-release: hdmed_1.0.1.zip, r-oldrel: hdmed_1.0.1.zip |
| macOS binaries: | r-release (arm64): hdmed_1.0.1.tgz, r-oldrel (arm64): hdmed_1.0.1.tgz, r-release (x86_64): hdmed_1.0.1.tgz, r-oldrel (x86_64): hdmed_1.0.1.tgz |
| Old sources: | hdmed archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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