priormix: Construction of an Empirical based prior

In NPflow: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Description

Construction of an Empirical based prior

Usage

priormix(sDPMclust, nu0add = 5)

Arguments

sDPMclust	an object of class summary.DPMMclust
nu0add	an additional value integer added to hyperprior parameter nu (increase to avoid non positive definite matrix sampling)

See Also

summary.DPMMclust

Examples

rm(list=ls())

#Number of data
n <- 2000
set.seed(123)
#set.seed(4321)


d <- 2
ncl <- 4

# Sample data

sdev <- array(dim=c(d,d,ncl))

xi <- matrix(nrow=d, ncol=ncl, c(-1.5, 1.5, 1.5, 1.5, 2, -2.5, -2.5, -3))
#xi <- matrix(nrow=d, ncol=ncl, c(-0.5, 0, 0.5, 0, 0.5, -1, -1, 1))
psi <- matrix(nrow=d, ncol=4, c(0.4, -0.6, 0.8, 0, 0.3, -0.7, -0.3, -0.8))
nu <- c(100,15,8,5)
p <- c(0.15, 0.05, 0.5, 0.3) # frequence des clusters
sdev[, ,1] <- matrix(nrow=d, ncol=d, c(0.3, 0, 0, 0.3))
sdev[, ,2] <- matrix(nrow=d, ncol=d, c(0.1, 0, 0, 0.3))
sdev[, ,3] <- matrix(nrow=d, ncol=d, c(0.3, 0.15, 0.15, 0.3))
sdev[, ,4] <- .3*diag(2)


c <- rep(0,n)
w <- rep(1,n)
z <- matrix(0, nrow=d, ncol=n)
for(k in 1:n){
 c[k] = which(rmultinom(n=1, size=1, prob=p)!=0)
 w[k] <- rgamma(1, shape=nu[c[k]]/2, rate=nu[c[k]]/2)
 z[,k] <- xi[, c[k]] + psi[, c[k]]*rtruncnorm(n=1, a=0, b=Inf, mean=0, sd=1/sqrt(w[k])) +
                (sdev[, , c[k]]/sqrt(w[k]))%*%matrix(rnorm(d, mean = 0, sd = 1), nrow=d, ncol=1)
 #cat(k, "/", n, " observations simulated\n", sep="")
}

# Set parameters of G0
hyperG0 <- list()
hyperG0[["b_xi"]] <- rowMeans(z)
hyperG0[["b_psi"]] <- rep(0,d)
hyperG0[["kappa"]] <- 0.001
hyperG0[["D_xi"]] <- 100
hyperG0[["D_psi"]] <- 100
hyperG0[["nu"]] <- d+1
hyperG0[["lambda"]] <- diag(apply(z,MARGIN=1, FUN=var))/3

 # hyperprior on the Scale parameter of DPM
 a <- 0.0001
 b <- 0.0001

 nbclust_init <- 30

if(interactive()){
 MCMCsample_st <- DPMGibbsSkewT(z, hyperG0, a, b, N=2000, doPlot=FALSE,
                                nbclust_init, diagVar=FALSE)
 s <- summary(MCMCsample_st, burnin = 1500, thin=5, posterior_approx=TRUE)
 pmix <- priormix(s)
}

NPflow documentation built on Feb. 6, 2020, 5:15 p.m.