PTolmm: Bayesian analysis for a semiparametric ordinal linear mixed...

In DPpackage: Bayesian Nonparametric Modeling in R

Description

This function generates a posterior density sample for a semiparametric ordinal linear mixed model, using a Mixture of Multivariate Polya Trees prior for the distribution of the random effects.

Usage

PTolmm(fixed,random,prior,mcmc,state,status,data=sys.frame(sys.parent()),
      na.action=na.fail)

Arguments

fixed	a two-sided linear formula object describing the fixed-effects part of the model, with the response on the left of a ~ operator and the terms, separated by + operators, on the right.
random	a one-sided formula of the form ~z1+...+zn | g, with z1+...+zn specifying the model for the random effects and g the grouping variable. The random effects formula will be repeated for all levels of grouping.
prior	a list giving the prior information. The list include the following parameter: a0 and b0 giving the hyperparameters for prior distribution of the precision parameter of the Polya Tree (PT) prior, alpha giving the value of the precision parameter (it must be specified if a0 and b0 are missing, see details below), nu0 and tinv giving the hyperparameters of the inverted Wishart prior distribution for the scale matrix of the normal baseline distribution, sigma giving the value of the covariance matrix of the centering distribution (it must be specified if nu0 and tinv are missing), mub and Sb giving the hyperparameters of the normal prior distribution for the mean of the normal baseline distribution, mu giving the value of the mean of the centering distribution (it must be specified if mub and Sb are missing), beta0 and Sbeta0 giving the hyperparameters of the normal prior distribution for the fixed effects (must be specified only if fixed effects are considered in the model), M giving the finite level of the PT prior to be considered, frstlprob a logical variable indicating whether the first level probabilities of the PT are fixed or not (the default is FALSE), and typepr indicating whether the type of decomposition of the centering covariance is random (1) or not (0).
mcmc	a list giving the MCMC parameters. The list must include the following integers: nburn giving the number of burn-in scans, nskip giving the thinning interval, nsave giving the total number of scans to be saved, ndisplay giving the number of saved scans to be displayed on screen (the function reports on the screen when every ndisplay iterations have been carried out), nbase giving the number scans to be performed before the parameters of the centering distribution and the precision parameter are updated (i.e., the update of this parameters is invoked only once in every nbase scans) (the default value is 1), tune1, tune2, and tune3, giving the Metropolis tuning parameter for the baseline mean, variance, and precision parameter, respectively. If tune1, tune2, or tune3 are not specified or negative, an adpative Metropolis algorithm is performed. Finally, the integer samplef indicates whether the functional parameters must be sample (1) or not (0).
state	a list giving the current value of the parameters. This list is used if the current analysis is the continuation of a previous analysis.
status	a logical variable indicating whether this run is new (TRUE) or the continuation of a previous analysis (FALSE). In the latter case the current value of the parameters must be specified in the object state.
data	data frame.
na.action	a function that indicates what should happen when the data contain NAs. The default action (na.fail) causes PTolmm to print an error message and terminate if there are any incomplete observations.

Details

This generic function fits an ordinal linear mixed-effects model with a probit link and a Mixture of Multivariate Polya Trees prior (see, Lavine 1992; 1994, for details about univariate PT) for the distribution of the random effects as described in Jara, Hanson and Lessaffre (2009):

Yij = k, if gammak-1 ≤q Wij < gammak, k=1,…,K

Wij | betaF, betaR , bi ~ N(Xij betaF + Zij betaR + Zij bi, 1), i=1,…,N, j=1,…,ni

thetai | G ~ G

G | alpha,mu,Sigma,O ~ PT^M(Pi^{mu,Sigma,O},A)

where, thetai = betaR + bi, beta = betaF, and O is an orthogonal matrix defining the decomposition of the centering covariance matrix. As in Hanson (2006), the PT prior is centered around a N_d(mu,Sigma) distribution. However, we consider the class of partitions Pi^{mu,Sigma, O}. The partitions starts with base sets that are Cartesian products of intervals obtained as quantiles from the standard normal distribution. A multivariate location-scale transformation, theta=mu+Sigma^{1/2} z, is applied to each base set yielding the final sets. Here Sigma^{1/2}=T'O' where T is the unique upper triangular Cholesky matrix of Sigma. The family A={alphae: e \in E*}, where E*=U_{m=0}^{M} E_d^m, with E_d and E_m the d-fold product of E=\{0,1\} and the the m-fold product of E_d, respectively. The family A was specified as alpha{e1 … em}=α m^2.

To complete the model specification, independent hyperpriors are assumed,

alpha | a0, b0 ~ Gamma(a0,b0)

beta | beta0, Sbeta0 ~ N(beta0,Sbeta0)

mu | mub, Sb ~ N(mub,Sb)

Sigma | nu0, T ~ IW(nu0,T)

O ~ Haar(q)

A uniform prior is used for the cutoff points. Note that the inverted-Wishart prior is parametrized such that E(Sigma)= T^{-1}/(nu0-q-1).

The precision or total mass parameter, α, of the DP prior can be considered as random, having a gamma distribution, Gamma(a0,b0), or fixed at some particular value.

The computational implementation of the model is based on the marginalization of the PT as descried in Jara, Hanson and Lessaffre (2009).

Value

An object of class PTolmm representing the linear mixed-effects model fit. Generic functions such as print, plot, and summary have methods to show the results of the fit. The results include betaR, betaF, mu, the elements of Sigma, alpha, and ortho.

The function PTrandom can be used to extract the posterior mean of the random effects.

The list state in the output object contains the current value of the parameters necessary to restart the analysis. If you want to specify different starting values to run multiple chains set status=TRUE and create the list state based on this starting values. In this case the list state must include the following objects:

alpha	giving the value of the precision parameter
b	a matrix of dimension (nsubjects)*(nrandom effects) giving the value of the random effects for each subject.
cutoff	a real vector defining the cutoff points. Note that the first cutoff must be fixed at 0 in this function.
beta	giving the value of the fixed effects.
mu	giving the mean of the normal baseline distributions.
sigma	giving the variance matrix of the normal baseline distributions.
ortho	giving the orthogonal matrix H, used in the decomposition of the covariance matrix.

Author(s)

Alejandro Jara <[e-mail]>

Tim Hanson <[e-mail]>

References

Hanson, T. (2006) Inference for Mixtures of Finite Polya Trees. Journal of the American Statistical Association, 101: 1548-1565.

Jara, A., Hanson, T., Lesaffre, E. (2009) Robustifying Generalized Linear Mixed Models using a New Class of Mixtures of Multivariate Polya Trees. Journal of Computational and Graphical Statistics, 18(4): 838-860.

Lavine, M. (1992) Some aspects of Polya tree distributions for statistical modelling. The Annals of Statistics, 20: 1222-11235.

Lavine, M. (1994) More aspects of Polya tree distributions for statistical modelling. The Annals of Statistics, 22: 1161-1176.

See Also

PTrandom, PTlmm , PTglmm, DPMglmm, DPMlmm, DPMolmm, DPlmm , DPglmm, DPolmm

Examples

## Not run: 

    # Schizophrenia Data
      data(psychiatric)
      attach(psychiatric)

    # Prior information
      prior <- list(M=4,
                    frstlprob=FALSE,
                    alpha=1,
                    nu0=4.01,
                    tinv=diag(1,1),
                    mub=rep(0,1),
                    Sb=diag(100,1),
                    beta0=rep(0,3),
                    Sbeta0=diag(1000,3))

    # MCMC parameters
      mcmc <- list(nburn=10000,
                   nsave=10000,
                   nskip=20,
                   ndisplay=100,
                   samplef=1)

    # Initial state
      state <- NULL

    # Fitting the model
      fit1 <- PTolmm(fixed=imps79o~sweek+tx+sweek*tx,random=~1|id,prior=prior,
                     mcmc=mcmc,state=state,status=TRUE)
      fit1

    # Summary with HPD and Credibility intervals
      summary(fit1)
      summary(fit1,hpd=FALSE)

    # Plot model parameters
      plot(fit1)

    # Plot an specific model parameter
      plot(fit1,ask=FALSE,nfigr=1,nfigc=2,param="sigma-(Intercept)")	

    # Extract random effects
      PTrandom(fit1)

    # Extract predictive information of random effects
      aa<-PTrandom(fit1,predictive=TRUE)
      aa

    # Predictive marginal and joint distributions      
      plot(aa)

## End(Not run)

DPpackage documentation built on May 1, 2019, 10:23 p.m.