#' @title High-Dimensional Mediation Analysis for 'Omic' Data
#'
#' @description
#' HIMA is an R package for estimating and testing high-dimensional mediation effects in omic studies.
#' HIMA can perform high-dimensional mediation analysis on a wide range of omic data types as
#' potential mediators, including epigenetics, transcriptomics, proteomics, metabolomics, and microbiomics.
#' HIMA can also handle survival data mediation analysis and perform quantile mediation analysis.
#'
#' \tabular{ll}{ Package: \tab HIMA\cr Type: \tab Package\cr
#' Version: \tab 2.2.2\cr Date: \tab 2024-08-24\cr License: \tab GPL-3\cr }
#'
#' @name HIMA-package
#'
#' @aliases HIMA-package HIMA
#'
#' @details
#' # If package "qvalue" is not found during installation, please first install "qvalue" package
#' # through Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/qvalue.html
#'
#' @author
#' Yinan Zheng \email{y-zheng@@northwestern.edu},
#' Haixiang Zhang \email{haixiang.zhang@@tju.edu.cn},
#' Lei liu (Contact) \email{lei.liu@@wustl.edu}
#'
#' Maintainer: Yinan Zheng \email{y-zheng@@northwestern.edu}
#'
#' @references
#' 1. Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L,
#' Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies.
#' Bioinformatics. 2016. DOI: 10.1093/bioinformatics/btw351. PMID: 27357171; PMCID: PMC5048064
#'
#' 2. Zhang H, Zheng Y, Hou L, Zheng C, Liu L. Mediation Analysis for Survival Data with High-Dimensional Mediators.
#' Bioinformatics. 2021. DOI: 10.1093/bioinformatics/btab564. PMID: 34343267; PMCID: PMC8570823
#'
#' 3. Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation Effect Selection in High-dimensional and Compositional Microbiome data.
#' Stat Med. 2021. DOI: 10.1002/sim.8808. PMID: 33205470; PMCID: PMC7855955
#'
#' 4. Zhang H, Chen J, Li Z, Liu L. Testing for Mediation Effect with Application to Human Microbiome Data.
#' Stat Biosci. 2021. DOI: 10.1007/s12561-019-09253-3. PMID: 34093887; PMCID: PMC8177450
#'
#' 5. Perera C, Zhang H, Zheng Y, Hou L, Qu A, Zheng C, Xie K, Liu L. HIMA2: High-dimensional Mediation Analysis and Its Application in
#' Epigenome-wide DNA Methylation Data. BMC Bioinformatics. 2022. DOI: 10.1186/s12859-022-04748-1. PMID: 35879655; PMCID: PMC9310002
#'
#' 6. Zhang H, Hong X, Zheng Y, Hou L, Zheng C, Wang X, Liu L. High-Dimensional Quantile Mediation Analysis with Application to a Birth
#' Cohort Study of Mother–Newborn Pairs. Bioinformatics. 2024. DOI: 10.1093/bioinformatics/btae055. PMID: 38290773; PMCID: PMC10873903
#'
#' 7. Bai X, Zheng Y, Hou L, Zheng C, Liu L, Zhang H. An Efficient Testing Procedure for High-dimensional Mediators with FDR Control.
#' Statistics in Biosciences. 2024. DOI: 10.1007/s12561-024-09447-4.
#'
#' @keywords package
#'
#' @import ncvreg
#' @import glmnet
#'
#' @importFrom utils packageVersion
#' @importFrom stats p.adjust rnorm runif rbinom lm glm model.matrix BIC coef ls.diag lsfit pnorm complete.cases rgamma
#' @importFrom iterators idiv nextElem
#' @importFrom parallel detectCores
#' @importFrom foreach foreach %dopar% registerDoSEQ getDoParWorkers
#' @importFrom doParallel registerDoParallel
#' @importFrom HDMT fdr_est
#' @importFrom hdi lasso.proj
#' @importFrom conquer conquer.cv.reg
#' @importFrom quantreg rq
#' @importFrom survival Surv coxph
#' @importFrom MASS mvrnorm glm.nb
#' @importFrom hommel hommel discoveries
#'
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