mlm4omics
This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see mlm4omics.
Multilevel Model for Multivariate Responses with Missing Values
Bioconductor version: 3.10
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("mlm4omics")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mlm4omics")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mlm4omics")| Introduction of mlm4omics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, CopyNumberVariation, ImmunoOncology, MassSpectrometry, Proteomics, Regression, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| 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 |
| System Requirements | GNU make |
| URL | https://doi.org/10.1101/153049 |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) |
| Linking To | StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mlm4omics_1.3.0.tar.gz |
| Windows Binary | mlm4omics_1.3.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | mlm4omics_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mlm4omics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mlm4omics |
| Bioc Package Browser | https://code.bioconductor.org/browse/mlm4omics/ |
| Package Short Url | https://bioconductor.org/packages/mlm4omics/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |