mlm4omics

DOI: 10.18129/B9.bioc.mlm4omics    

Multilevel Model for Multivariate Responses with Missing Values

Bioconductor version: Release (3.8)

To conduct Bayesian inference regression for responses with multilevel explanatory variables and missing values; It uses function from 'Stan', a software to implement posterior sampling using Hamiltonian MC and its variation Non-U-Turn algorithms. It implements the posterior sampling of regression coefficients from the multilevel regression models. The package has two main functions to handle not-missing-at-random missing responses and left-censored with not-missing-at random responses. The purpose is to provide a similar format as the other R regression functions but using 'Stan' models.

Author: Irene Zeng [aut, cre], Thomas Lumley [ctb]

Maintainer: Irene SL Zeng <i.zeng at auckland.ac.nz>

Citation (from within R, enter citation("mlm4omics")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("mlm4omics", version = "3.8")

Documentation

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Text   NEWS

Details

biocViews Bayesian, Classification, CopyNumberVariation, MassSpectrometry, Proteomics, Regression, Software
Version 1.0.0
License GPL-3
Depends R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats
Imports rstan (>= 2.17.3), rstantools (>= 1.5.0), MASS, Matrix, stats4, ggplot2
LinkingTo StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0)
Suggests testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0)
SystemRequirements GNU make
Enhances
URL https://doi.org/10.1101/153049
Depends On Me
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary mlm4omics_1.0.0.zip
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/mlm4omics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mlm4omics
Package Short Url http://bioconductor.org/packages/mlm4omics/
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