https://github.com/cran/cplm
Revision 9be3f5a0653739a591e2b30cc9e77900612dad9a authored by Wayne Zhang on 08 November 2011, 00:00:00 UTC, committed by Gabor Csardi on 08 November 2011, 00:00:00 UTC
1 parent 31a5c50
Tip revision: 9be3f5a0653739a591e2b30cc9e77900612dad9a authored by Wayne Zhang on 08 November 2011, 00:00:00 UTC
version 0.4-1
version 0.4-1
Tip revision: 9be3f5a
bcpglm_lat.c
/************************************************************/
/* Function for the Markov Chain Monte Carlo algorithm */
/* in the Compound Poisson Generalized Linear Model */
/* using the latent variable approach */
/* Author: Wayne Zhang */
/* actuary_zhang@hotmail.com */
/************************************************************/
/**
* @file bcpglm_lat.c
* @brief Function for implementing the MCMC algorithm
* in the Compound Poisson Generalized Linear Model using
* the latent variable approach
* @author Wayne Zhang
*/
#include "cplm.h"
/** struct used in cpglm_bayes */
typedef struct {
da_parm *dap ; /**< struct to store data and parameters */
int *simTvec ; /**< vector of simulated latent variables */
double *pbeta_mean ; /**< vector of prior means for beta */
double *pbeta_var ; /**< vector of prior variance for beta */
double *mu ; /**< mean vector */
double *eta ; /**< linear predictor */
double bound_phi ; /**< bound for phi */
double *bound_p ; /**< bound for p */
double mh_p_var ; /**< proposal variance in M-H update for p */
double mh_phi_var ; /**< proposal variance in M-H update for phi */
double *mh_beta_var ; /**< proposal covariance matrix in M-H update for beta */
} bcpglm_str;
/************************************************/
/* Function to compute full conditionals */
/************************************************/
/**
* posterior log density of the index parameter p
*
* @param x value of p at which the log density is to be calculated
* @param data a void struct, cocerced to bcpglm_str internally
*
* @return log posterior density
*/
static double bcpglm_post_p_lat(double x, void *data){
bcpglm_str *da = data ;
double ld = cplm_llikS(da->mu, da->dap->phi, x,
da->simTvec, da->dap) ;
return ld ;
}
/**
* posterior log density of the dispersion parameter phi
*
* @param x value of phi at which the log density is to be calculated
* @param data a void struct, cocerced to bcpglm_str internally
*
* @return log posterior density
*/
static double bcpglm_post_phi_lat(double x, void *data){
bcpglm_str *da = data ;
da_parm *dap = da->dap ;
int i, kk ;
double ld=0, p2=2-dap->p, p1=dap->p-1 ;
for (i=0; i<dap->nO; i++)
ld += pow(da->mu[i],p2) * dap->weights[i];
ld /= (- x*p2) ;
for (i=0; i<dap->nP; i++){
kk = dap->ygt0[i] ;
ld += - dap->Y[kk]*pow(da->mu[kk],-p1)*dap->weights[kk] /(x*p1)
- log(x)* da->simTvec[i]/p1;
}
return ld ;
}
/**
* posterior log density of of the vector of beta
*
* @param x vector of values for beta
* @param data void struct that is coerced to bcpglm_str
*
* @return log posterior density for beta
*/
double bcpglm_post_beta_lat(double *x, void *data){
bcpglm_str *da = data ;
da_parm *dap = da->dap ;
int i, kk, nO=dap->nO, nB=dap->nB ;
double ld=0, p2=2-dap->p, p1=dap->p-1,
*beta_old = dap->beta;
// update mu
dap->beta = x ;
cpglm_fitted(da->eta, da->mu, (double *) NULL, dap);
dap->beta = beta_old ;
// loglikelihood from data
for (i=0; i<nO; i++)
ld += pow(da->mu[i],p2) * dap->weights[i];
ld /= (- dap->phi*p2) ;
for (i=0; i<dap->nP; i++){
kk = dap->ygt0[i] ;
ld += - dap->Y[kk]*pow(da->mu[kk],-p1)*
dap->weights[kk] /(dap->phi*p1);
}
// prior info
for (i=0;i<nB;i++)
ld += -0.5*(x[i]-da->pbeta_mean[i])*
(x[i]-da->pbeta_mean[i])/da->pbeta_var[i] ;
return ld ;
}
/************************************************/
/* Main function to fit compound Poisson */
/* GLM using Monte Carlo Markov Chains */
/************************************************/
/**
* MCMC simulation for compound Poisson GLM
*
* @param da a bcpglm_str struct
* @param nR report interval
* @param nit number of iterations
* @param nbn number of burn-ins
* @param nth thinning rate
* @param sims a 2d array to store simulation results
* @param acc_pct acceptance percentage
*
*/
static void bcpglm_mcmc_lat(bcpglm_str *da, int nR, int nit, int nbn,
int nth, double **sims, double *acc_pct){
da_parm *dap = da->dap ;
int nP = dap->nP, nB=dap->nB ;
double xtemp, *beta_sim ;
double xl_p = da->bound_p[0], xr_p=da->bound_p[1],
xr_phi = da->bound_phi, p_sd = sqrt(da->mh_p_var),
phi_sd= sqrt(da->mh_phi_var) ;
int acc, accept[]={0,0,0};
int i, j, iter, ns ;
beta_sim = Alloca(nB, double) ;
R_CheckStack() ;
GetRNGstate() ;
for (iter=0;iter<nit;iter++){
if (nR>0 && (iter+1)%nR==0)
Rprintf("Iteration: %d \n ", iter+1) ;
R_CheckUserInterrupt() ;
// update latent variable T using rejection sampling
for (i=0;i<nP;i++){
da->dap->k=i ;
cplm_rlatT_reject(1, &(da->simTvec[i]), da->dap) ;
}
R_CheckUserInterrupt() ;
// M-H update of p using truncated normal
acc = metrop_tnorm_rw(dap->p, p_sd, xl_p, xr_p, &xtemp,
bcpglm_post_p_lat, (void *) da);
dap->p = xtemp ;
accept[0] += acc ;
R_CheckUserInterrupt() ;
//Metropolis-Hasting block update
acc = metrop_mvnorm_rw(nB, dap->beta, da->mh_beta_var,
beta_sim, bcpglm_post_beta_lat, (void *)da) ;
Memcpy(dap->beta, beta_sim, nB) ;
accept[1] += acc ;
cpglm_fitted(da->eta, da->mu, (double*) NULL, dap) ;
R_CheckUserInterrupt() ;
// M-H update of phi using truncated normal
acc = metrop_tnorm_rw(dap->phi, phi_sd, 0, xr_phi, &xtemp,
bcpglm_post_phi_lat, (void *) da);
dap->phi = xtemp ;
accept[2] += acc ;
R_CheckUserInterrupt() ;
// print out acceptance rate if necessary
if (nR>0 && (iter+1)%nR==0){
Rprintf(_("Acceptance rate: beta(%4.2f%%), phi(%4.2f%%), p(%4.2f%%),\n"),
accept[1]*1.0/(iter+1)*100, accept[2]*1.0/(iter+1)*100,
accept[0]*1.0/(iter+1)*100 );
}
// store results
if (iter>=nbn && (iter+1-nbn)%nth==0 ){
ns = (iter+1-nbn)/nth -1;
for (j=0;j<nB;j++)
sims[ns][j] = dap->beta[j];
sims[ns][nB] = dap->phi ;
sims[ns][nB+1] = dap->p ;
}
}
PutRNGstate() ;
// compute acceptance percentage
for (i=0;i<3;i++)
acc_pct[i] = accept[i]*1.0/nit ;
}
/**
* implement MCMC for compound Poisson GLM using latent variables
*
* @param x a list object
*
* @return the simulated values
*
*/
SEXP bcpglm_gibbs_lat (SEXP x){
// get dimensions
int *dm = DIMS_ELT(x) ;
int nO = dm[nO_POS], nP = dm[nP_POS],
nB = dm[nB_POS], nit = dm[itr_POS],
nbn = dm[bun_POS], nth = dm[thn_POS],
nS = dm[kp_POS], nR = dm[rpt_POS],
tn = dm[tnit_POS], ntn = dm[ntn_POS];
int i, j, k;
double acc_pct[]={0,0,0}, *init, **sims,
tnw = REAL(getListElement(x,"tune.weight"))[0];
SEXP inits = getListElement(x,"inits"), ans, ans_tmp;
//allocate memory for struct and simulated values
bcpglm_str *da = (bcpglm_str *) R_alloc(1,sizeof(bcpglm_str)) ;
da_parm *dap = (da_parm *) R_alloc(1,sizeof(da_parm)) ;
da->dap = dap ;
da->simTvec = ivect(nP) ;
// fill in struct dap
dap->nO = nO ;
dap->nP = nP;
dap->nB = nB ;
dap->ygt0 = YPO_ELT(x) ;
dap->Y= Y_ELT(x) ;
dap->offset= OFFSET_ELT(x) ;
dap->weights= PWT_ELT(x) ;
dap->X = X_ELT(x) ;
dap->link_power = LKP_ELT(x)[0] ;
dap->beta = BETA_ELT(x) ;
dap->phi = PHI_ELT(x)[0] ;
dap->p = P_ELT(x)[0];
// fill in struct da
da->mu = MU_ELT(x) ;
da->eta = ETA_ELT(x) ;
da->pbeta_mean = PBM_ELT(x) ;
da->pbeta_var = PBV_ELT(x) ;
da->mh_beta_var = EBV_ELT(x);
da->mh_p_var = EPV_ELT(x)[0];
da->mh_phi_var = EPHIV_ELT(x)[0];
da->bound_p = BDP_ELT(x) ;
da->bound_phi = BDPHI_ELT(x)[0] ;
// update eta and mu
cpglm_fitted(da->eta, da->mu, (double*) NULL, dap) ;
// tune the scale parameter for M-H update
if (tn){
int etn = ceil(tn *1.0/ntn) ; // # iters per tuning loop
double *beta_sims = dvect(etn*nB), *p_sims = dvect(etn),
*phi_sims = dvect(etn), sam_p_var, sam_phi_var,
*sam_beta_var = dvect(nB*nB) ;
sims = dmatrix(etn,nB+2) ;
if (nR>0)
Rprintf("Tuning phase...\n");
for (k=0;k<ntn;k++) {
bcpglm_mcmc_lat(da, 0, etn, 0, 1, sims, acc_pct);
// convert to long vector
for (i=0;i<etn;i++){
p_sims[i] = sims[i][nB+1] ;
phi_sims[i] = sims[i][nB] ;
for (j=0;j<nB;j++)
beta_sims[i+j*etn] = sims[i][j] ;
}
// adjust proposal variance for p and phi
cov(etn,1,p_sims, &sam_p_var) ;
cov(etn,1,phi_sims, &sam_phi_var) ;
if (acc_pct[0]<0.4 || acc_pct[0] > 0.6)
da->mh_p_var = tnw * da->mh_p_var + (1-tnw) * sam_p_var ;
if (acc_pct[2]<0.4 || acc_pct[2] > 0.6)
da->mh_phi_var = tnw * da->mh_phi_var + (1-tnw) * sam_phi_var ;
// adjust vcov for beta
cov(etn, nB, beta_sims, sam_beta_var) ;
if (acc_pct[1]<0.15 || acc_pct[1] > 0.35){
for (i=0;i<nB*nB;i++)
da->mh_beta_var[i] = tnw * da->mh_beta_var[i] + (1-tnw) * sam_beta_var[i];
}
}
if (nR>0){
Rprintf("Acceptance rate in the last tuning phase: beta(%4.2f%%), phi(%4.2f%%), p(%4.2f%%)\n",
acc_pct[1]*100, acc_pct[2]*100, acc_pct[0]*100);
Rprintf("-----------------------------------------\n");
}
}
// run Markov chains
PROTECT(ans=allocVector(VECSXP,dm[chn_POS])) ;
if (nR>0){
Rprintf("Markov Chain Monte Carlo starts...\n");
Rprintf("-----------------------------------------\n");
}
// simulations
sims = dmatrix(nS,nB+2) ;
for (k=0;k<dm[chn_POS];k++){
if (nR>0)
Rprintf("Start Markov chain %d\n", k+1);
// re-initialize
init = REAL(VECTOR_ELT(inits,k));
dap->beta = init ;
dap->phi = init[nB] ;
dap->p = init[nB+1];
// update eta and mu
cpglm_fitted(da->eta, da->mu, (double*) NULL, dap) ;
bcpglm_mcmc_lat(da, nR, nit, nbn, nth, sims,acc_pct );
//return result
PROTECT(ans_tmp=allocMatrix(REALSXP, nS, nB+2));
for (j=0;j<nB+2;j++){
for (i=0;i<nS;i++)
REAL(ans_tmp)[i+nS*j]= sims[i][j] ;
}
SET_VECTOR_ELT(ans, k, ans_tmp);
UNPROTECT(1) ;
if (nR>0)
Rprintf("-----------------------------------------\n");
}
UNPROTECT(1) ;
if (nR>0)
Rprintf("Markov Chain Monte Carlo ends!\n");
return ans ;
}
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