VsusP

Introduction

In the context of Gaussian linear models, the package proposes a solution of the variable selection problem using Shrinkage priors. First obtain a posterior distribution of the number of significant variables by clustering the significant variables and the noise coefficients and obtaining samples from this distribution using MCMC. Then, the significant variables are estimated from the posterior median of absolute beta. This approach requires only one tuning parameters and is applicable to continuous shrinkage priors as well.

Getting Started

These instructions will install the package to your computer.

Prerequisites

In order to install the package directly from Github, you need to have the devtools package:

install.packages("devtools")

Installation

To install the package from Github, first load devtools:

library(devtools)

Next, install VsusP as follows:

devtools::install_github("nilson01/VsusP")

The package can now be loaded into R and used:

library(VsusP)

Example

To provide an example of the VsusP package, we will first simulate some data:

# install.packages("MASS") # if not yet installed
library(MASS)
set.seed(20221208)
sim.XY <- function(n, p, beta) {
  X <- matrix(rnorm(n * p), n, p)
  Y <- as.vector(X %*% beta + rnorm(n, 0, 1))
  return(list(X = X, Y = Y, beta = beta))
}

n <- 100
p <- 20
beta <- exp(rnorm(p))
data <- sim.XY(n, p, beta)

The function Sequential2Means is used get the samples of Beta and H.b.i. Beta can be calculated using different shrinkage priors and gibbs sampling technique, whereas H.b.i is the estimated number of signals corresponding to each tuning parameter b.i that is computed using S2M algorithm. If the Beta matrix is available prior, then H.b.i is recommended to be computed using Sequential2MeansBeta.

b.i <- seq(0, 1, 0.05)
S2M <- Sequential2Means(X = data$X, Y = data$Y, b.i = b.i, prior = "horseshoe+", n.samples = 5000, burnin = 2000)
Beta <- S2M$Beta
H.b.i <- S2M$H.b.i

Then, using the result from Sequential2Means or Sequential2MeansBeta, appropriate tuning parameter can be estimated using b.i Vs H.b.i plot from OptimalHbi function.

OptimalHbi(bi = b.i, Hbi = H.b.i)

Finally, the indices of important subset of variables can be obtained using S2MVarSelection function. The input parameter H is the optimal H.b.i value from the selected tuning parameter in OptimalHbi function. Also, Beta is the user defined matrix or the matrix derived from Sequential2Means function.

H <- 17
impVariablesGLM <- S2MVarSelection(Beta, H)
impVariablesGLM

There are several other variants of these functions as per input cases. For example: Sequential2MeansBeta and S2MVarSelectionV1. Check the documentation for the different functions on options and details, using e.g., ?Sequential2Means.

References

R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Li, H., & Pati, D. (2020) “Variable Selection Using Shrinkage Priors.” Computational Statistics & Data Analysis, 107, pp.107-119. doi:10.1016/j.csda.2020.106839.