HDP {bbricks}R Documentation

Create objects of type "HDP".


Create an object of type "HDP", which represents the Hierarchical-Dirichlet-Process conjugate structure:

G|gamma \sim DP(gamma,U)

pi_j|G,alpha \sim DP(alpha,G), j = 1:J

z|pi_j \sim Categorical(pi_j)

k|z,G \sim Categorical(G), \textrm{ if z is a sample from the base measure G}

theta_k|psi \sim H0(psi)

x|theta_k,k \sim F(theta_k)

where DP(gamma,U) is a Dirichlet Process on positive integers, gamma is the "concentration parameter", U is the "base measure" of this Dirichlet process, U is an uniform distribution on all positive integers. DP(alpha,G) is a Dirichlet Process on integers with concentration parameter alpha and base measure G. The choice of F() and H0() can be described by an arbitrary "BasicBayesian" object such as "GaussianGaussian","GaussianInvWishart","GaussianNIW", "GaussianNIG", "CatDirichlet", and "CatDP". See ?BasicBayesian for definition of "BasicBayesian" objects, and see for example ?GaussianGaussian for specific "BasicBayesian" instances. As a summary, An "HDP" object is simply a combination of a "CatHDP" object (see ?CatHDP) and an object of any "BasicBayesian" type.
In the case of HDP, z and k can only be positive integers.
This object will be used as a place for recording and accumulating information in the related inference/sampling functions such as posterior(), posteriorDiscard(), dPosteriorPredictive(), rPosteriorPredictive() and so on.


  objCopy = NULL,
  ENV = parent.frame(),
  gamma = list(gamma = 1, j = 2L, alpha = 1, H0aF = "GaussianNIW", parH0 = list(m = 0, k
    = 1, v = 2, S = 1))



an object of type "HDP". If "objCopy" is not NULL, the function create a new "HDP" object by copying the content from objCopy, otherwise this new object will be created by using "ENV" and "gamma". Default NULL.


environment, specify where the object will be created.


list, a named list of parameters, gamma=list(gamma,alpha,j,H0aF,parH0). Where gamma$gamma is a numeric value specifying the concentration parameter of DP(gamma,U), gamma$alpha is a numeric value specifying the concentration parameter of DP(alpha,G), gamma$j is the number of groups J. gamma$H0aF is the name of the "BasicBayesian" object which specifies the structure of H0() and F(). gamma$parH0 is the parameters passed to the selected H0aF. For example, if gamma$H0aF="GaussianNIW", then gamma$parH0 should be a named list of NIW parameters: gamma$parH0=list(m,k,v,S), where gamma$parH0$m is a numeric "location" parameter; gamma$parH0$S is a symmetric positive definite matrix representing the "scale" parameters; gamma$parH0$k and gamma$parH0$v are numeric values.


An object of class "HDP".


Teh, Yee W., et al. "Sharing clusters among related groups: Hierarchical Dirichlet processes." Advances in neural information processing systems. 2005.

See Also

BasicBayesian,GaussianNIW,GaussianNIG,CatDirichlet,CatHDP,posterior.HDP,posteriorDiscard.HDP,marginalLikelihood.HDP ...


## This is an example of Gibbs sampling on an hierarchical mixture model,
## using Hierarchical Dirichlet Process.

## load some hierarchical mixture data, check ?mmhData for details.
x <- mmhData$x
js <- mmhData$groupLabel

## Step1: initialize--------------------------------------------------
z <- rep(1L,nrow(x))
k <- rep(1L,nrow(x))
## create a HDP object to track all the changes
obj <- HDP(gamma = list(gamma=1,j=max(js),alpha=1,
ss <- sufficientStatistics(obj$H,x=x,foreach = TRUE) #sufficient statistics
N <- length(ss)
for(i in 1L:N){# initialize k and z
    tmp <- rPosteriorPredictive(obj = obj,n=1,x=x[i,,drop=FALSE],j=js[i])
    z[i] <- tmp["z"]
    k[i] <- tmp["k"]
    posterior.HDP(obj = obj,ss = ss[[i]],ss1 = k[i],ss2 = z[i],j = js[i])

## Step2: main Gibbs loop---------------------------------------------
maxit <- 20                             #iterative for maxit times
it <- 0                                 #iteration tracker
pb <- txtProgressBar(min = 0,max = maxit,style = 3)
    for(i in 1L:N){
        ## remove the sample from the posterior info
        posteriorDiscard(obj = obj,ss = ss[[i]],ss1=k[i],ss2=z[i],j=js[i])
        ## resample a new partition
        tmp <- rPosteriorPredictive(obj = obj,n=1,x=x[i,,drop=FALSE],j=js[i])
        z[i] <- tmp["z"]
        k[i] <- tmp["k"]
        posterior(obj = obj,ss = ss[[i]], ss1=k[i],ss2 = z[i],j=js[i])
    plot(x=x[,1],y=x[,2],col=k)         #to visualize the group label dynamics
    it <- it+1

[Package bbricks version 0.1.4 Index]