Package rewind details

Reconstructing Etiology with Binary Decomposition

This package implememnts a Bayesian hierarchical model that represents observations as aggregation of a few unobserved binary machines where the aggregation varies by subjects. Our approach is to specify the model likelihood via factorization into two latent binary matrices: machine profiles and individual factors. Given latent factorization, we account for inherent errors in measurement using sensitivities and specificities of protein detection. We use a prior for the individual factor matrix (Indian Buffet Process for binary matrices) to encourage a small number of subject clusters each with distinct patterns of active machines. The posterior distribution for the numbers of patient clusters and machines are estimated from data and by design tend to concentrate on smaller values. The posterior distributions of model parameters are estimated via Markov chain Monte Carlo which makes a list of molecular machine profiles with uncertainty quantification as well as patient-specific posterior probability of having each machine.

Maintainer: Zhenke Wu < zhenkewu at umich.edu >

 
From within R, enter citation('rewind')


To cite package 'rewind' in publications use:

Zhenke Wu and Scott Zeger (2019). rewind: Reconstructing Etiology
with Binary Decomposition. R package version 0.6.2.
https://github.com/zhenkewu/rewind

A BibTeX entry for LaTeX users is

@Manual{,
title = {rewind: Reconstructing Etiology with Binary Decomposition},
author = {Zhenke Wu and Scott Zeger},
year = {2019},
note = {R package version 0.6.2},
url = {https://github.com/zhenkewu/rewind},
}

 

If you have any problems with this package you can open a new issue or check the already existing ones here.

 
 
To install this package, start R and enter:

source("https://oslerinhealth.org/oslerLite.R")

# Default Install
osler_install('rewind')

# from GitHub
osler_install('rewind', release = "stable", release_repo = "github")
osler_install('rewind', release = "current", release_repo = "github")

More detailed installation instructions can be found here.

 

Initially submitted on October 7 2019 3:32PM
Last updated on October 7 2019 3:32PM
Package type standard
Source GitHub https://github.com/zhenkewu/rewind GitHub
OslerinHealth GitHub https://github.com/oslerinhealth/rewind GitHub
DependsR (3.4.0)
ImportsmatrixStats (0.52.2), Rcpp (0.12.15), stats (3.4.1), graphics (3.4.1), grDevices (3.4.1)
LinkingToRcpp, RcppArmadillo
Suggestsknitr, testthat, bibtex, knitcitations, rmarkdown, ars (0.5), RcppArmadillo (0.8.300.1.0), mcclust.ext (1.0)