R/rhierMnlRwMixture_rcpp.r

Defines functions rhierMnlRwMixture

Documented in rhierMnlRwMixture

rhierMnlRwMixture=function(Data,Prior,Mcmc){
#
# revision history:
#   12/04 changed by rossi to fix bug in drawdelta when there is zero/one unit in a mixture component
#   09/05 added loglike output, changed to reflect new argument order in llmnl, mnlHess 
#   12/05 changed weighting scheme to (1-w)logl_i + w*Lbar (normalized) 
#   03/07 added classes
#   09/08 changed Dirichlet a check
#   04/15 by Wayne Taylor: added nprint option to MCMC argument
#   07/16 by Wayne Taylor: added sign restrictions
#   10/10 by Dan Yavorsky: changed default priors when sign restrictions imposed
#
# purpose: run hierarchical mnl logit model with mixture of normals 
#   using RW and cov(RW inc) = (hess_i + Vbeta^-1)^-1
#   uses normal approximation to pooled likelihood
#
# Arguments:
#   Data contains a list of (p,lgtdata, and possibly Z)
#      p is number of choice alternatives
#      lgtdata is a list of lists (one list per unit)
#          lgtdata[[i]]=list(y,X)
#             y is a vector indicating alternative chosen
#               integers 1:p indicate alternative
#             X is a length(y)*p x nvar matrix of values of
#               X vars including intercepts
#             Z is an length(lgtdata) x nz matrix of values of variables
#               note: Z should NOT contain an intercept
#   Prior contains a list of (deltabar,Ad,mubar,Amu,nu,V,ncomp,SignRes) 
#      ncomp is the number of components in normal mixture
#           if elements of Prior (other than ncomp) do not exist, defaults are used
#      SignRes is a vector of sign restrictions
#   Mcmc contains a list of (s,c,R,keep,nprint)
#
# Output:  as list containing
#   Deltadraw R/keep  x nz*nvar matrix of draws of Delta, first row is initial value
#   betadraw is nlgt x nvar x R/keep array of draws of betas
#   probdraw is R/keep x ncomp matrix of draws of probs of mixture components
#   compdraw is a list of list of lists (length R/keep)
#      compdraw[[rep]] is the repth draw of components for mixtures
#   loglike  log-likelikelhood at each kept draw
#
# Priors:
#    beta_i = D %*% z[i,] + u_i
#       u_i ~ N(mu_ind[i],Sigma_ind[i])
#       ind[i] ~multinomial(p)
#       p ~ dirichlet (a)
#       D is a k x nz array
#          delta= vec(D) ~ N(deltabar,A_d^-1)
#    mu_j ~ N(mubar,A_mu^-1(x)Sigma_j)
#    Sigma_j ~ IW(nu,V^-1)
#    ncomp is number of components
#
# MCMC parameters
#   s is the scaling parameter for the RW inc covariance matrix; s^2 Var is inc cov
#      matrix
#   w is parameter for weighting function in fractional likelihood
#      w is the weight on the normalized pooled likelihood 
#   R is number of draws
#   keep is thinning parameter, keep every keepth draw
#   nprint - print estimated time remaining on every nprint'th draw
#
#  check arguments
#
if(missing(Data)) {pandterm("Requires Data argument -- list of p,lgtdata, and (possibly) Z")}
  if(is.null(Data$p)) {pandterm("Requires Data element p (# choice alternatives)") }
  p=Data$p
  if(is.null(Data$lgtdata)) {pandterm("Requires Data element lgtdata (list of data for each unit)")}
  lgtdata=Data$lgtdata
  nlgt=length(lgtdata)
  drawdelta=TRUE
if(is.null(Data$Z)) { cat("Z not specified",fill=TRUE); fsh() ; drawdelta=FALSE}
  else {if (!is.matrix(Data$Z)) {pandterm("Z must be a matrix")}
    else {if (nrow(Data$Z) != nlgt) {pandterm(paste("Nrow(Z) ",nrow(Z),"ne number logits ",nlgt))}
      else {Z=Data$Z}}}
  if(drawdelta) {
     nz=ncol(Z)
     colmeans=apply(Z,2,mean)
     if(sum(colmeans) > .00001) 
       {pandterm(paste("Z does not appear to be de-meaned: colmeans= ",colmeans))}
  }
#
# check lgtdata for validity
#
ypooled=NULL
Xpooled=NULL
if(!is.null(lgtdata[[1]]$X & is.matrix(lgtdata[[1]]$X))) {oldncol=ncol(lgtdata[[1]]$X)}
for (i in 1:nlgt) 
{
    if(is.null(lgtdata[[i]]$y)) {pandterm(paste0("Requires element y of lgtdata[[",i,"]]"))}
    if(is.null(lgtdata[[i]]$X)) {pandterm(paste0("Requires element X of lgtdata[[",i,"]]"))}
    if(!is.matrix(lgtdata[[i]]$X)) {pandterm(paste0("lgtdata[[",i,"]]$X must be a matrix"))}
    if(!is.vector(lgtdata[[i]]$y, mode = "numeric") & !is.vector(lgtdata[[i]]$y, mode = "logical") & !is.matrix(lgtdata[[i]]$y)) 
      {pandterm(paste0("lgtdata[[",i,"]]$y must be a numeric or logical vector or matrix"))}
    if(is.matrix(lgtdata[[i]]$y)) { if(ncol(lgtdata[[i]]$y)>1) { pandterm(paste0("lgtdata[[",i,"]]$y must be a vector or one-column matrix")) } }
    ypooled=c(ypooled,lgtdata[[i]]$y)
    nrowX=nrow(lgtdata[[i]]$X)
    if((nrowX/p) !=length(lgtdata[[i]]$y)) {pandterm(paste("nrow(X) ne p*length(yi); exception at unit",i))}
    newncol=ncol(lgtdata[[i]]$X)
    if(newncol != oldncol) {pandterm(paste("All X elements must have same # of cols; exception at unit",i))}
    Xpooled=rbind(Xpooled,lgtdata[[i]]$X)
    oldncol=newncol
}
nvar=ncol(Xpooled)
levely=as.numeric(levels(as.factor(ypooled)))
if(length(levely) != p) {pandterm(paste("y takes on ",length(levely)," values -- must be = p"))}
bady=FALSE
for (i in 1:p )
{
    if(levely[i] != i) bady=TRUE
}
cat("Table of Y values pooled over all units",fill=TRUE)
print(table(ypooled))
if (bady) 
  {pandterm("Invalid Y")}
#
# check on prior
#
if(missing(Prior)) {pandterm("Requires Prior list argument (at least ncomp)")} 
if(is.null(Prior$ncomp)) {pandterm("Requires Prior element ncomp (num of mixture components)")} else {ncomp=Prior$ncomp}
if(is.null(Prior$SignRes)) {SignRes=rep(0,nvar)} else {SignRes=Prior$SignRes}                     
if(length(SignRes) != nvar) {pandterm("The length SignRes must be equal to the dimension of X")}
if(sum(!(SignRes %in% c(-1,0,1))>0)) {pandterm("All elements of SignRes must be equal to -1, 0, or 1")}
if(is.null(Prior$mubar) & sum(abs(SignRes))==0) {
  mubar=matrix(rep(0,nvar),nrow=1)
  } else { 
  if(is.null(Prior$mubar) & sum(abs(SignRes)) >0) {
  mubar=matrix(rep(0,nvar)+2*abs(SignRes),nrow=1)
  } else { 
  mubar=matrix(Prior$mubar,nrow=1) } }
if(ncol(mubar) != nvar) {pandterm(paste("mubar must have ncomp cols, ncol(mubar)= ",ncol(mubar)))}
if(is.null(Prior$Amu) & sum(abs(SignRes))==0) {
  Amu=matrix(BayesmConstant.A,ncol=1)
  } else {
  if(is.null(Prior$Amu) & sum(abs(SignRes)) >0) {
  Amu=matrix(BayesmConstant.A*10,ncol=1)
  } else {Amu=matrix(Prior$Amu,ncol=1) } }
if(ncol(Amu) != 1 | nrow(Amu) != 1) {pandterm("Am must be a 1 x 1 array")}
if(is.null(Prior$nu) & sum(abs(SignRes))==0) {
  nu=nvar+BayesmConstant.nuInc
  } else {
  if(is.null(Prior$nu) & sum(abs(SignRes)) >0) {
  nu=nvar+BayesmConstant.nuInc+12
  } else {
  nu=Prior$nu } }
if(nu < 1) {pandterm("invalid nu value")}
if(is.null(Prior$V) & sum(abs(SignRes))==0) {
  V=nu*diag(nvar)
  } else {
  if(is.null(Prior$V) & sum(abs(SignRes)) >0) {
  V=nu*diag(abs(SignRes)*0.1+(!abs(SignRes))*4)
  } else {
  V=Prior$V } }
if(sum(dim(V)==c(nvar,nvar)) !=2) pandterm("Invalid V in prior")
if(is.null(Prior$Ad) & drawdelta) {Ad=BayesmConstant.A*diag(nvar*nz)} else {Ad=Prior$Ad}
if(drawdelta) {if(ncol(Ad) != nvar*nz | nrow(Ad) != nvar*nz) {pandterm("Ad must be nvar*nz x nvar*nz")}}
if(is.null(Prior$deltabar)& drawdelta) {deltabar=rep(0,nz*nvar)} else {deltabar=Prior$deltabar}
if(drawdelta) {if(length(deltabar) != nz*nvar) {pandterm("deltabar must be of length nvar*nz")}}
if(is.null(Prior$a)) { a=rep(BayesmConstant.a,ncomp)} else {a=Prior$a}
if(length(a) != ncomp) {pandterm("Requires dim(a)= ncomp (no of components)")}
bada=FALSE
for(i in 1:ncomp) { if(a[i] < 0) bada=TRUE}
if(bada) pandterm("invalid values in a vector")
    
if(is.null(Prior$nu)&sum(abs(SignRes))>0) {nu = nvar+15}                                        
if(is.null(Prior$Amu)&sum(abs(SignRes))>0) {Amu = matrix(.1)}                                   
if(is.null(Prior$V)&sum(abs(SignRes))>0) {V = nu*(diag(nvar)-diag(abs(SignRes)>0)*.8)} 

#
# check on Mcmc
#
if(missing(Mcmc)) 
  {pandterm("Requires Mcmc list argument")}
else 
   { 
    if(is.null(Mcmc$s)) {s=BayesmConstant.RRScaling/sqrt(nvar)} else {s=Mcmc$s}
    if(is.null(Mcmc$w)) {w=BayesmConstant.w}  else {w=Mcmc$w}
    if(is.null(Mcmc$keep)) {keep=BayesmConstant.keep} else {keep=Mcmc$keep}
    if(is.null(Mcmc$R)) {pandterm("Requires R argument in Mcmc list")} else {R=Mcmc$R}
    if(is.null(Mcmc$nprint)) {nprint=BayesmConstant.nprint} else {nprint=Mcmc$nprint}
      if(nprint<0) {pandterm('nprint must be an integer greater than or equal to 0')}
    }
#
# print out problem
#
cat(" ",fill=TRUE)
cat("Starting MCMC Inference for Hierarchical Logit:",fill=TRUE)
cat("   Normal Mixture with",ncomp,"components for first stage prior",fill=TRUE)
cat(paste("  ",p," alternatives; ",nvar," variables in X"),fill=TRUE)
cat(paste("   for ",nlgt," cross-sectional units"),fill=TRUE)
cat(" ",fill=TRUE)
cat("Prior Parms: ",fill=TRUE)
cat("nu =",nu,fill=TRUE)
cat("V ",fill=TRUE)
print(V)
cat("mubar ",fill=TRUE)
print(mubar)
cat("Amu ", fill=TRUE)
print(Amu)
cat("a ",fill=TRUE)
print(a)
if(drawdelta) 
{
   cat("deltabar",fill=TRUE)
   print(deltabar)
   cat("Ad",fill=TRUE)
   print(Ad)
}
cat(" ",fill=TRUE)
cat("MCMC Parms: ",fill=TRUE)
cat(paste("s=",round(s,3)," w= ",w," R= ",R," keep= ",keep," nprint= ",nprint),fill=TRUE)
cat("",fill=TRUE)

oldbetas = matrix(double(nlgt * nvar), ncol = nvar)

#--------------------------------------------------------------------------------------------------
#
#  create functions needed
#
llmnlFract=                                                           
  function(beta,y,X,betapooled,rootH,w,wgt,SignRes = rep(0,ncol(X))){ 
    z=as.vector(rootH%*%(beta-betapooled))
    return((1-w)*llmnl_con(beta,y,X,SignRes)+w*wgt*(-.5*(z%*%z)))
  }

mnlHess_con=function (betastar, y, X, SignRes = rep(0,ncol(X))) {     
  
  #Reparameterize beta to betastar to allow for sign restrictions
  beta = betastar
  beta[SignRes!=0] = SignRes[SignRes!=0]*exp(beta[SignRes!=0])
  
  n = length(y)
  j = nrow(X)/n
  k = ncol(X)
  Xbeta = X %*% beta
  Xbeta = matrix(Xbeta, byrow = T, ncol = j)
  Xbeta = exp(Xbeta)
  iota = c(rep(1, j))
  denom = Xbeta %*% iota
  Prob = Xbeta/as.vector(denom)
  Hess = matrix(double(k * k), ncol = k)
  for (i in 1:n) {
    p = as.vector(Prob[i, ])
    A = diag(p) - outer(p, p)
    Xt = X[(j * (i - 1) + 1):(j * i), ]
    Hess = Hess + crossprod(Xt, A) %*% Xt
  }
  return(Hess)
}

#-------------------------------------------------------------------------------------------------------
#
# intialize compute quantities for Metropolis
#
cat("initializing Metropolis candidate densities for ",nlgt," units ...",fill=TRUE)
fsh()
#
#  now go thru and computed fraction likelihood estimates and hessians
#
#       Lbar=log(pooled likelihood^(n_i/N))
#
#       fraction loglike = (1-w)*loglike_i + w*Lbar
#
betainit=c(rep(0,nvar))
#
#  compute pooled optimum
#
out=optim(betainit,llmnl_con,method="BFGS",control=list( fnscale=-1,trace=0,reltol=1e-6), 
          X=Xpooled,y=ypooled,SignRes=SignRes)                                            
betapooled=out$par
H=mnlHess_con(betapooled,ypooled,Xpooled,SignRes)                                         
rootH=chol(H)
for (i in 1:nlgt) 
{
   wgt=length(lgtdata[[i]]$y)/length(ypooled)
   out=optim(betapooled,llmnlFract,method="BFGS",control=list( fnscale=-1,trace=0,reltol=1e-4), 
             X=lgtdata[[i]]$X,y=lgtdata[[i]]$y,betapooled=betapooled,rootH=rootH,w=w,wgt=wgt,SignRes=SignRes)
   if(out$convergence == 0) { 
     hess=mnlHess_con(out$par,lgtdata[[i]]$y,lgtdata[[i]]$X,SignRes)                              
     lgtdata[[i]]=c(lgtdata[[i]],list(converge=1,betafmle=out$par,hess=hess)) }
   else
     { lgtdata[[i]]=c(lgtdata[[i]],list(converge=0,betafmle=c(rep(0,nvar)),
        hess=diag(nvar))) }
   oldbetas[i,]=lgtdata[[i]]$betafmle
   if(i%%50 ==0) cat("  completed unit #",i,fill=TRUE)
   fsh()
}
#
#  initialize values
#
# set initial values for the indicators
#     ind is of length(nlgt) and indicates which mixture component this obs
#     belongs to.
#
ind=NULL
ninc=floor(nlgt/ncomp)
for (i in 1:(ncomp-1)) {ind=c(ind,rep(i,ninc))}
if(ncomp != 1) {ind = c(ind,rep(ncomp,nlgt-length(ind)))} else {ind=rep(1,nlgt)}
#
# initialize probs
#
oldprob=rep(1/ncomp,ncomp)
#
#initialize delta
#
if (drawdelta){
  olddelta = rep(0,nz*nvar)
} else { #send placeholders to the _loop function if there is no Z matrix
  olddelta = 0
  Z = matrix(0)
  deltabar = 0
  Ad = matrix(0)
}

###################################################################
# Wayne Taylor
# 09/22/2014
###################################################################
draws =  rhierMnlRwMixture_rcpp_loop(lgtdata, Z,
                                     deltabar, Ad, mubar, Amu,
                                     nu, V, s,
                                     R, keep, nprint, drawdelta,
                                     as.matrix(olddelta), a, oldprob, oldbetas, ind, SignRes)
####################################################################

if(drawdelta){
  attributes(draws$Deltadraw)$class=c("bayesm.mat","mcmc")
  attributes(draws$Deltadraw)$mcpar=c(1,R,keep)}
attributes(draws$betadraw)$class=c("bayesm.hcoef")
attributes(draws$nmix)$class="bayesm.nmix"

return(draws)
}

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bayesm documentation built on July 21, 2017, 7:18 p.m.