MCMCpack/src/cMCMClogit.cc

//////////////////////////////////////////////////////////////////////////
// cMCMClogit.cc is C++ code to estimate a logistic regression model with
//   a multivariate normal prior
//
// Andrew D. Martin
// Dept. of Political Science
// Washington University in St. Louis
// admartin@wustl.edu
//
// Kevin M. Quinn
// Dept. of Government
// Harvard University
// kevin_quinn@harvard.edu
//
// This software is distributed under the terms of the GNU GENERAL
// PUBLIC LICENSE Version 2, June 1991.  See the package LICENSE
// file for more information.
//
// updated to the new version of Scythe 7/25/2004 KQ
//
// Copyright (C) 2003-2007 Andrew D. Martin and Kevin M. Quinn
// Copyright (C) 2007-present Andrew D. Martin, Kevin M. Quinn,
//    and Jong Hee Park
//////////////////////////////////////////////////////////////////////////


#ifndef CMCMCLOGIT_CC
#define CMCMCLOGIT_CC

#include <iostream>
#include "MCMCrng.h"
#include "MCMCfcds.h"
#include "matrix.h"
#include "distributions.h"
#include "stat.h"
#include "la.h"
#include "ide.h"
#include "smath.h"

#include <R.h>           // needed to use Rprintf()
#include <R_ext/Utils.h> // needed to allow user interrupts

using namespace scythe;
using namespace std;

static double
logit_logpost(const Matrix<>& Y, const Matrix<>& X, const Matrix<>& beta,
              const Matrix<>& beta_prior_mean,
              const Matrix<>& beta_prior_prec)
{
  // likelihood
  const Matrix<> eta = X * beta;
  const Matrix<> p = 1.0 / (1.0 + exp(-eta));
  double loglike = 0.0;

  for (unsigned int i = 0; i < Y.rows(); ++ i)
    loglike += Y(i) * ::log(p(i)) + (1 - Y(i)) * ::log(1 - p(i));

  //prior
  double logprior = 0.0;
  if (beta_prior_prec(0) != 0)
    logprior = lndmvn(beta, beta_prior_mean, invpd(beta_prior_prec));

  return (loglike + logprior);
}

template <typename RNGTYPE>
void
MCMClogit_impl (rng<RNGTYPE>& stream, const Matrix<>& Y,
                const Matrix<>& X, const Matrix<>& tune, Matrix<>& beta,
                const Matrix<>& b0, const Matrix<>& B0,
                const Matrix<>& V, unsigned int burnin, unsigned int mcmc,
                unsigned int thin, unsigned int verbose,
                Matrix<>& result)
{

  // define constants
  const unsigned int tot_iter = burnin + mcmc;  // total mcmc iterations
  const unsigned int k = X.cols();

  // proposal parameters
  const Matrix<> propV = tune * invpd(B0 + invpd(V)) * tune;
  const Matrix<> propC = cholesky(propV) ;

  double logpost_cur = logit_logpost(Y, X, beta, b0, B0);

  // MCMC loop
  unsigned int count = 0;
  unsigned int accepts = 0;
  for (unsigned int iter = 0; iter < tot_iter; ++iter) {

    // sample beta
    const Matrix<> beta_can = gaxpy(propC, stream.rnorm(k, 1, 0, 1), beta);

    const double logpost_can = logit_logpost(Y, X, beta_can, b0, B0);
    const double ratio = ::exp(logpost_can - logpost_cur);

    if (stream.runif() < ratio) {
      beta = beta_can;
      logpost_cur = logpost_can;
      ++accepts;
    }

    // store values in matrices
    if (iter >= burnin && ((iter % thin) == 0)) {
        result(count++, _) = beta;
    }

    // print output to stdout
    if(verbose > 0 && iter % verbose == 0){
      Rprintf("\n\nMCMClogit iteration %i of %i \n", (iter+1), tot_iter);
      Rprintf("beta = \n");
      for (unsigned int j = 0; j < k; ++j)
        Rprintf("%10.5f\n", beta(j));
      Rprintf("Metropolis acceptance rate for beta = %3.5f\n\n",
        static_cast<double>(accepts) / static_cast<double>(iter+1));
    }

    R_CheckUserInterrupt(); // allow user interrupts

  }// end MCMC loop
  if (verbose > 0){
    Rprintf("\n\n@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n");
    Rprintf("The Metropolis acceptance rate for beta was %3.5f",
	    static_cast<double>(accepts) / static_cast<double>(tot_iter));
    Rprintf("\n@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n");
  }
}

extern "C"{

  void cMCMClogit(double *sampledata, const int *samplerow,
		             const int *samplecol, const double *Ydata,
                 const int *Yrow, const int *Ycol, const double *Xdata,
                 const int *Xrow, const int *Xcol, const int *burnin,
                 const int *mcmc, const int *thin, const double *tunedata,
                 const int *tunerow, const int *tunecol,
                 const int *uselecuyer, const int *seedarray,
                 const int *lecuyerstream, const int *verbose,
                 const double *betastartdata, const int *betastartrow,
                 const int *betastartcol, const double *b0data,
                 const int *b0row, const int *b0col, const double *B0data,
                 const int *B0row, const int *B0col, const double *Vdata,
                 const int *Vrow, const int *Vcol)
  {

    // pull together Matrix objects
    Matrix<> Y(*Yrow, *Ycol, Ydata);
    Matrix<> X(*Xrow, *Xcol, Xdata);
    Matrix<> tune(*tunerow, *tunecol, tunedata);
    Matrix<> beta(*betastartrow, *betastartcol, betastartdata);
    Matrix<> b0(*b0row, *b0col, b0data);
    Matrix<> B0(*B0row, *B0col, B0data);
    Matrix<> V(*Vrow, *Vcol, Vdata);

    Matrix<> result(*samplerow, *samplecol, false);
    MCMCPACK_PASSRNG2MODEL(MCMClogit_impl, Y, X, tune, beta, b0, B0, V,
                           *burnin, *mcmc, *thin, *verbose, result);

    unsigned int size = *samplecol * *samplerow;
    for (unsigned int i = 0; i < size; ++i)
      sampledata[i] = result(i);
  }
}

#endif