CSDPbinary: Bayesian analysis for a semiparametric logistic regression...
In DPpackage: Bayesian Nonparametric Modeling in R

Description Usage Arguments Details Value Author(s) References Examples

This function generates a posterior density sample for a semiparametric binary regression model using a Centrally Standarized Dirichlet process prior for the link function.

1 2	CSDPbinary(formula,baseline="logistic",prior,mcmc,state,status,misc=NULL, data=sys.frame(sys.parent()),na.action=na.fail)

`formula`	a two-sided linear formula object describing the model fit, with the response on the left of a `~` operator and the terms, separated by `+` operators, on the right.
`baseline`	a description of the baseline error distribution to be used in the model. The baseline distributions considered by `CSDPbinary` so far is logistic.
`prior`	a list giving the prior information. The list includes the following parameters: a0 and b0 giving the hyperparameters for prior distribution of the precision parameter of the Centrally-Standarized Dirichlet process prior, alpha giving the value of the precision parameter (it must be specified if a0 and b0 are missing, see the details below), and beta0 and Sbeta0 giving the hyperparameters of the normal prior distribution for the regression coefficients.
`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, ntheta giving the thinning interval for the theta parameter (if missing, the value 1 is considered), ndisplay giving the number of saved scans to be displayed on the screen (the function reports on the screen when every ndisplay iterations have been carried out), and tune giving the Metropolis tuning parameter (the default value is 1.1).
`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.
`misc`	misclassification information. When used, this list must include two objects, sens and spec, giving the sensitivity and specificity, respectively. Both can be a vector or a scalar. This information is used to correct for misclassification in the conditional bernoulli model.
`data`	data frame.
`na.action`	a function that indicates what should happen when the data contain `NA`s. The default action (`na.fail`) causes `CSDPbinary` to print an error message and terminate if there are any incomplete observations.

This generic function fits a semiparametric binary regression model using a Centrally-Standarized Dirichlet Process Prior (CSDP) (Newton, Czado and Chappell, 1996):

yi = I(Vi <= Xi β),\ i=1,…,n

V1,…,Vn | G ~ G

G | m, p, d, h ~ CSDP(m,p,d,h)

where, m={m1,m2,m3,m4} is the base measure, mj≤ft(B \right)=alpha G0≤ft(B\right)I{Aj≤ft(theta\right)},

A1 ≤ft(theta \right) = (-∞,theta-d ], A2 ≤ft(theta \right) = (theta-d,0 ]

A3 ≤ft(theta \right) = (0,theta ], A4 ≤ft(theta \right) = (theta,∞),

and h is a uniform distribution on (0,d). Note that in the construction of Newton et al. (1996), G=((1-2)/2)*(G1+G4)+(p/2)*(G2+G3), where Gj are conditionally independent Dirichlet processes with base measure mj.

To complete the model specification, the following prior distributions are assumed,

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

β | beta0, Sbeta0 ~ N(beta0,Sbeta0)

The precision parameter, alpha, of the CSDP prior can be considered as random, having a Gamma distribution, Gamma(a0,b0), or fixed at some particular value. When alpha is random a strategy similar to the method described by Escobar and West (1995) is used. To let alpha to be fixed at a particular value, set a0 to NULL in the prior specification.

A Metropolis-Hastings step is used to sample the fully conditional distribution of the regression coefficients and errors (see, Jara, Garcia-Zattera and Lesaffre, 2006). In the computational implementation of the model, G is considered as latent data and sampled partially with sufficient accuracy to be able to generate V1,…,Vn+1 which are exactly iid G, as proposed by Doss (1994). Both Ferguson's definition of DP and the Sethuraman-Tiwari (1982) representation of the process are used, as described in Jara, Garcia-Zattera and Lesaffre (2006). An extra step which moves the clusters in such a way that the posterior distribution is still a stationary distribution, is performed in order to improve the rate of mixing.

An object of class CSDPbinary representing the semiparametric logistic regression model fit. Generic functions such as print, plot, predict, summary, and anova have methods to show the results of the fit. The results include beta, the precision parameter (alpha), the number of clusters (ncluster), and the link function.

The MCMC samples of the parameters and the errors in the model are stored in the object thetasave and randsave, respectively. Both objects are included in the list save.state and are matrices which can be analyzed directly by functions provided by the coda package.

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:

`beta`	giving the value of the regression coefficients.
`theta`	giving the value of the third quartile parameter.
`v`	giving the value of the errors (it must be consistent with yi = I(Vi < xi beta).

`y`	giving the value of the true response binary variable (only if the model considers correction for misclassification).
`alpha`	giving the value of the precision parameter.

Alejandro Jara <atjara@uc.cl>

Doss, H. (1994) Bayesian nonparametric estimation for incomplete data using mixtures of Dirichlet priors. The Annals of Statistics, 22: 1763 - 1786.

Escobar, M.D. and West, M. (1995) Bayesian Density Estimation and Inference Using Mixtures. Journal of the American Statistical Association, 90: 577-588.

Jara, A., Garcia-Zattera, M.J., Lesaffre, E. (2006) Semiparametric Bayesian Analysis of Misclassified Binary Data. XXIII International Biometric Conference, July 16-21, Montréal, Canada.

Newton, M.A., Czado, C., and Chappell, R. (1996) Bayesian inference for semiparametric binary regression. Journal of the American Statistical Association, 91, 142-153.

Sethuraman, J., and Tiwari, R. C. (1982) Convergence of Dirichlet Measures and the Interpretation of their Parameter, in Statistical Decision Theory and Related Topics III (vol. 2), eds. S. S. Gupta and J. O. Berger, New York: Academic Press, pp. 305 - 315.

## Not run: 
    # Bioassay Data Example
    # Cox, D.R. and Snell, E.J. (1989). Analysis of Binary Data. 2nd ed. 
    # Chapman and Hall. p. 7. 
    # In this example there are 150 subjects at 5 different stimulus 
    # levels, 30 at each level.


      y<-c(rep(0,30-2),rep(1,2),
           rep(0,30-8),rep(1,8),
           rep(0,30-15),rep(1,15),
           rep(0,30-23),rep(1,23),
           rep(0,30-27),rep(1,27))

      x<-c(rep(0,30),
           rep(1,30),
           rep(2,30),
           rep(3,30),
           rep(4,30))


    # Initial state
      state <- NULL

    # MCMC parameters
      nburn<-5000
      nsave<-10000
      nskip<-10
      ntheta<-1
      ndisplay<-100
      mcmc <- list(nburn=nburn,nsave=nsave,nskip=nskip,
                   ntheta=ntheta,ndisplay=ndisplay,tune=1.1)


    # Prior distribution
      prior <- list(alpha=1, d=2*log(3), p=0.5, beta0=rep(0,2), 
                    Sbeta0=diag(1000,2))

    # Fitting the model

      fit1 <- CSDPbinary(y~x,prior=prior,mcmc=mcmc,state=state,
                         status=TRUE) 
      fit1

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

    # Plot model parameters (to see the plots gradually set ask=TRUE)
      plot(fit1)

    # Plot an specific model parameter (to see the plots gradually 
    # set ask=TRUE)
      plot(fit1,ask=FALSE,nfigr=1,nfigc=2,param="x")	
      plot(fit1,ask=FALSE,param="link",nfigc=1,nfigr=1)

    # Table of Pseudo Contour Probabilities
      anova(fit1)

    # Predictive Distribution
      npred<-40  
      xnew<-cbind(rep(1,npred),seq(0,4,length=npred))

      pp<-predict(fit1,xnew)       

      plot(seq(0,4,length=npred),pp$pmean,type='l',ylim=c(0,1),
           xlab="log2(concentration)",ylab="Probability")
      
    # Adding MLE estimates
      points(c(0,1,2,3,4),c(0.067,0.267,0.500,0.767,0.900),col="red")


## End(Not run)