bama - High Dimensional Bayesian Mediation Analysis

Perform mediation analysis in the presence of high-dimensional mediators based on the potential outcome framework. Bayesian Mediation Analysis (BAMA), developed by Song et al (2019) <doi:10.1111/biom.13189> and Song et al (2020) <arXiv:2009.11409>, relies on two Bayesian sparse linear mixed models to simultaneously analyze a relatively large number of mediators for a continuous exposure and outcome assuming a small number of mediators are truly active. This sparsity assumption also allows the extension of univariate mediator analysis by casting the identification of active mediators as a variable selection problem and applying Bayesian methods with continuous shrinkage priors on the effects.

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cpp

4.35 score 45 scripts 378 downloads

lodi - Limit of Detection Imputation for Single-Pollutant Models

Impute observed values below the limit of detection (LOD) via censored likelihood multiple imputation (CLMI) in single-pollutant models, developed by Boss et al (2019) <doi:10.1097/EDE.0000000000001052>. CLMI handles exposure detection limits that may change throughout the course of exposure assessment. 'lodi' provides functions for imputing and pooling for this method.

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3.74 score 1 stars 11 scripts 166 downloads

subgxe - Combine Multiple GWAS by Using Gene-Environment Interactions

Classical methods for combining summary data from genome-wide association studies (GWAS) only use marginal genetic effects and power can be compromised in the presence of heterogeneity. 'subgxe' is a R package that implements p-value assisted subset testing for association (pASTA), a method developed by Yu et al (2019) <doi:10.1159/000496867>. pASTA generalizes association analysis based on subsets by incorporating gene-environment interactions into the testing procedure.

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3.70 score 3 scripts 162 downloads

messi - Mediation with External Summary Statistic Information

Fits the MESSI, hard constraint, and unconstrained models in Boss et al. (2023) <doi:10.48550/arXiv.2306.17347> for mediation analyses with external summary-level information on the total effect.

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2.70 score 2 scripts 185 downloads

medScan - Large Scale Single Mediator Hypothesis Testing

A collection of methods for large scale single mediator hypothesis testing. The six included methods for testing the mediation effect are Sobel's test, Max P test, joint significance test under the composite null hypothesis, high dimensional mediation testing, divide-aggregate composite null test, and Sobel's test under the composite null hypothesis. Du et al (2023) <doi:10.1002/gepi.22510>.

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2.70 score 5 scripts 175 downloads

gigg - Group Inverse-Gamma Gamma Shrinkage for Sparse Regression with Grouping Structure

A Gibbs sampler corresponding to a Group Inverse-Gamma Gamma (GIGG) regression model with adjustment covariates. Hyperparameters in the GIGG prior specification can either be fixed by the user or can be estimated via Marginal Maximum Likelihood Estimation. Jonathan Boss, Jyotishka Datta, Xin Wang, Sung Kyun Park, Jian Kang, Bhramar Mukherjee (2021) <arXiv:2102.10670>.

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openblascpp

2.70 score 2 scripts 207 downloads