DPMGibbsSkewT_SeqPrior_parallel: Slice Sampling of Dirichlet Process Mixture of skew Student's...
In NPflow: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Description Usage Arguments Value Author(s) References Examples

Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions

DPMGibbsSkewT_SeqPrior_parallel(
  Ncpus,
  type_connec,
  z,
  prior_inform,
  hyperG0,
  N,
  nbclust_init,
  add.vagueprior = TRUE,
  weightnoninfo = NULL,
  doPlot = FALSE,
  plotevery = N/10,
  diagVar = TRUE,
  verbose = TRUE,
  monitorfile = "",
  ...
)

`Ncpus`	the number of processors available
`type_connec`	The type of connection between the processors. Supported cluster types are `"SOCK"`, `"FORK"`, `"MPI"`, and `"NWS"`. See also `makeCluster`.
`z`	data matrix `d x n` with `d` dimensions in rows and `n` observations in columns.
`prior_inform`	an informative prior such as the approximation computed by `summary.DPMMclust`.
`hyperG0`	prior mixing distribution.
`N`	number of MCMC iterations.
`nbclust_init`	number of clusters at initialization. Default to 30 (or less if there are less than 30 observations).
`add.vagueprior`	logical flag indicating whether a non informative component should be added to the informative prior. Default is `TRUE`.
`weightnoninfo`	a real between 0 and 1 giving the weights of the non informative component in the prior.
`doPlot`	logical flag indicating whether to plot MCMC iteration or not. Default to `TRUE`.
`plotevery`	an integer indicating the interval between plotted iterations when `doPlot` is `TRUE`.
`diagVar`	logical flag indicating whether the variance of each cluster is estimated as a diagonal matrix, or as a full matrix. Default is `TRUE` (diagonal variance).
`verbose`	logical flag indicating whether partition info is written in the console at each MCMC iteration.
`monitorfile`	a writable connections or a character string naming a file to write into, to monitor the progress of the analysis. Default is `""` which is no monitoring. See Details.
`...`	additional arguments to be passed to `plot_DPM`. Only used if `doPlot` is `TRUE`.

a object of class DPMclust with the following attributes:

mcmc_partitions:a list of length N. Each element mcmc_partitions[n] is a vector of length n giving the partition of the n observations.
alpha: a vector of length N. cost[j] is the cost associated to partition c[[j]]
U_SS_list:a list of length N containing the lists of sufficient statistics for all the mixture components at each MCMC iteration
weights_list:a list of length N containing the logposterior values at each MCMC iterations
logposterior_list:a list of length N containing the logposterior values at each MCMC iterations
data:the data matrix d x n with d dimensions in rows and n observations in columns
nb_mcmcit:the number of MCMC iterations
clust_distrib:the parametric distribution of the mixture component - "skewt"
hyperG0:the prior on the cluster location

Boris Hejblum

Hejblum BP, Alkhassim C, Gottardo R, Caron F and Thiebaut R (2019) Sequential Dirichlet Process Mixtures of Multivariate Skew t-distributions for Model-based Clustering of Flow Cytometry Data. The Annals of Applied Statistics, 13(1): 638-660. <doi: 10.1214/18-AOAS1209> <arXiv: 1702.04407> https://arxiv.org/abs/1702.04407 https://doi.org/10.1214/18-AOAS1209

rm(list=ls())

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


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))
#psi <- matrix(nrow=d, ncol=4, c(0.4, -0.6, 0.8, 0, 0.3, -0.7, -0.3, -0.8))
xi <- matrix(nrow=d, ncol=ncl, c(-0.2, 0.5, 2.4, 0.4, 0.6, -1.3, -0.9, -2.7))
psi <- matrix(nrow=d, ncol=4, c(0.3, -0.7, -0.8, 0, 0.3, -0.7, 0.2, 0.9))
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

 # do some plots
 nbclust_init <- 30

 ## Plot Data
 library(ggplot2)
 q <- (ggplot(data.frame("X"=z[1,], "Y"=z[2,]), aes(x=X, y=Y))
       + geom_point()
       + ggtitle("Simple example in 2d data")
       +xlab("D1")
       +ylab("D2")
       +theme_bw())
 q

if(interactive()){
 MCMCsample_st <- DPMGibbsSkewT(z, hyperG0, a, b, N=2000,
                                doPlot=TRUE, plotevery=250,
                                nbclust_init,
                                gg.add=list(theme_bw(),
                                 guides(shape=guide_legend(override.aes = list(fill="grey45")))),
                                diagVar=FALSE)
 s <- summary(MCMCsample_st, burnin = 1500, thin=5, posterior_approx=TRUE)
 F <- FmeasureC(pred=s$point_estim$c_est, ref=c)

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="")
}
MCMCsample_st2 <- DPMGibbsSkewT_SeqPrior_parallel(Ncpus=2, type_connec="SOCK",
                                                  z, prior_inform=s$param_posterior,
                                                  hyperG0, N=3000,
                                                  doPlot=TRUE, plotevery=100,
                                                  nbclust_init, diagVar=FALSE, verbose=FALSE,
                                                  gg.add=list(theme_bw(),
                                 guides(shape=guide_legend(override.aes = list(fill="grey45")))))
s2 <- summary(MCMCsample_st2, burnin = 2000, thin=5)
F2 <- FmeasureC(pred=s2$point_estim$c_est, ref=c)
}