miscF (version 0.1-5)

uvnm.rjmcmc: Univariate Normal Mixture (UVNM) Model with Unknown Number of Components

Description

Estimate the parameters of an univariate normal mixture model including the number of components using the Reversible Jump MCMC method. It can be used for density estimation and/or classification.

Usage

uvnm.rjmcmc(y, nsweep, kmax, k, w, mu, sigma2, Z,
              delta=1, xi=NULL, kappa=NULL, alpha=2,
              beta=NULL, g=0.2, h=NULL, verbose=TRUE)

Arguments

y

a vector of observations.

nsweep

number of sweeps. One sweep has six moves to update parameters including the number of components.

kmax

the maximum number of components.

k

initial value of number of components.

w

initial values of weights of different components.

mu

initial values of means of different components.

sigma2

initial values of variances of different components.

Z

initial values of allocations of all observations.

delta

the parameter of the prior distribution of w, the symmetric Dirichlet distribution. The default value is one.

xi

the mean of the prior distribution of means of components. By taking the default value NULL, it is set as the median of the data y internally.

kappa

the precision of the prior distribution of means of components. By taking the default value NULL, it is set as 1/R^2 internally, where R is the range of y.

alpha

the parameter shape of the prior distribution of precision of components. The default values is 2.

beta

the parameter rate of the prior distribution of precision of components. By taking the default value NULL, it is set as a number generated randomly from a gamma distribution with shape g and rate h.

g

the parameter shape of the gamma distribution for beta. The default value is 0.2.

h

the parameter rate of the gamma distribution for beta. By taking the default value NULL, it is set as 10/R^2 internally, where R is the range of y.

verbose

logical. If TRUE, then indicate the level of output after every 1000 sweeps. The default is TRUE.

Value

k.save

a vector of number of components.

w.save

weights of the UVNM, one component of the list per sweep.

mu.save

means of the UVNM, one component of the list per sweep.

sigma2.save

variances of the UVNM, one component of the list per sweep.

Z.save

a matrix of allocation, one column per sweep.

Details

Estimate the parameters of a univariate normal mixture model with flexible number of components using the Reversible Jump MCMC method in Richardson and Green (1997).

References

Sylvia Richardson and Peter J. Green (1997) On Bayesian Analysis of Mixtures with an Unknown Number of Components JRSSB vol. 59, no. 4 731-792

Sylvia Richardson and Peter J. Green (1998) Corrigendum: On Bayesian Analysis of Mixtures with an Unknown Number of Components JRSSB vol. 60, no. 3 661

See Also

NMixMCMC

Examples

# NOT RUN {
# }
# NOT RUN {
    require(mixAK)
    data(Acidity)
    y <- Acidity
    w <- c(0.50, 0.17, 0.33)
    mu <- c(4, 5, 6)
    sigma2 <- c(0.08, 0.10, 0.14)
    Z <- do.call(cbind, lapply(1:3, function(i)
                                    w[i]*dnorm(y, mu[i], sqrt(sigma2[i]))))
    Z <- apply(Z, 1, function(x) which(x==max(x))[1])
     
    result <- uvnm.rjmcmc(y, nsweep=200000, kmax=30, k=3,
                          w, mu, sigma2, Z)

    ksave <- result$k.save
    round(table(ksave[-(1:100000)])/100000,4)

    #conditional density estimation
    focus.k <- 3
    pick.k <- which(ksave==focus.k)
    w <- unlist(result$w.save[pick.k])
    mu <- unlist(result$mu.save[pick.k])
    sigma2 <- unlist(result$sigma2.save[pick.k])
    den.estimate <- rep(w, each=length(y)) *
                    dnorm(rep(y, length(w)), mean=rep(mu, each=length(y)),
                          sd=rep(sqrt(sigma2), each=length(y)))
    den.estimate <- rowMeans(matrix(den.estimate, nrow=length(y)))*focus.k

    #within-sample classification
    class <- apply(result$Z.save[,pick.k], 1,
                                function(x) c(sum(x==1), sum(x==2), sum(x==3)))
    class <- max.col(t(class))

    #visualize the results
    hist(y, freq=FALSE, breaks=20, axes=FALSE, ylim=c(-0.3, 1),
         main="Density Estimation and Classification", ylab="")
    axis(2, at=c(-(3:1)/10, seq(0,10,2)/10), labels=c(3:1, seq(0,10,2)/10),
         font=2)
    lines(sort(y), den.estimate[order(y)], col="red")
    for(i in 1:3){
        points(y[class==i], rep(-i/10, length(y[class==i])), col=i, pch=i)
    }
    mtext("Density", 2, at=0.5, line=2)
    mtext("Classification", 2, at=-0.15, line=2)
# }