dmeasure.c

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// dear emacs, please treat this as -*- C++ -*-
 
#include <R.h>
#include <Rmath.h>
#include <Rdefines.h>
 
 
#include "internal.h"
 
static R_INLINE SEXP add_args
(
 SEXP args, SEXP Onames, SEXP Snames,
 SEXP Pnames, SEXP Cnames, SEXP log
 ) {
  SEXP var;
  int v;
 
  // we construct the call from end to beginning
  // 'log', covariates, parameter, states, observables, then time
 
  // 'log' is a needed argument
  PROTECT(log = AS_LOGICAL(log));
  PROTECT(args = VectorToPairList(args));
  PROTECT(args = LCONS(log,args));
  SET_TAG(args,install("log"));
 
  // Covariates
  for (v = LENGTH(Cnames)-1; v >= 0; v--) {
    var = NEW_NUMERIC(1);
    args = LCONS(var,args);
    UNPROTECT(1);
    PROTECT(args);
    SET_TAG(args,installChar(STRING_ELT(Cnames,v)));
  }
 
  // Parameters
  for (v = LENGTH(Pnames)-1; v >= 0; v--) {
    var = NEW_NUMERIC(1);
    args = LCONS(var,args);
    UNPROTECT(1);
    PROTECT(args);
    SET_TAG(args,installChar(STRING_ELT(Pnames,v)));
  }
 
  // Latent state variables
  for (v = LENGTH(Snames)-1; v >= 0; v--) {
    var = NEW_NUMERIC(1);
    args = LCONS(var,args);
    UNPROTECT(1);
    PROTECT(args);
    SET_TAG(args,installChar(STRING_ELT(Snames,v)));
  }
 
  // Observables
  for (v = LENGTH(Onames)-1; v >= 0; v--) {
    var = NEW_NUMERIC(1);
    args = LCONS(var,args);
    UNPROTECT(1);
    PROTECT(args);
    SET_TAG(args,installChar(STRING_ELT(Onames,v)));
  }
 
  // Time
  var = NEW_NUMERIC(1);
  args = LCONS(var,args);
  UNPROTECT(1);
  PROTECT(args);
  SET_TAG(args,install("t"));
 
  UNPROTECT(3);
  return args;
 
}
static R_INLINE SEXP add_args {…}
 
static R_INLINE SEXP eval_call (
                                SEXP fn, SEXP args,
                                double *t,
                                double *y, int nobs,
                                double *x, int nvar,
                                double *p, int npar,
                                double *c, int ncov)
{
 
  SEXP var = args, ans, ob;
  int v;
 
  *(REAL(CAR(var))) = *t; var = CDR(var);
  for (v = 0; v < nobs; v++, y++, var=CDR(var)) *(REAL(CAR(var))) = *y;
  for (v = 0; v < nvar; v++, x++, var=CDR(var)) *(REAL(CAR(var))) = *x;
  for (v = 0; v < npar; v++, p++, var=CDR(var)) *(REAL(CAR(var))) = *p;
  for (v = 0; v < ncov; v++, c++, var=CDR(var)) *(REAL(CAR(var))) = *c;
 
  PROTECT(ob = LCONS(fn,args));
  PROTECT(ans = eval(ob,CLOENV(fn)));
 
  UNPROTECT(2);
  return ans;
 
}
static R_INLINE SEXP eval_call ( {…}
 
static R_INLINE SEXP ret_array (int nreps, int ntimes) {
  int dim[2] = {nreps, ntimes};
  const char *dimnm[2] = {".id","time"};
  SEXP F;
  PROTECT(F = makearray(2,dim));
  fixdimnames(F,dimnm,2);
  UNPROTECT(1);
  return F;
}
static R_INLINE SEXP ret_array (int nreps, int ntimes) {…}
 
SEXP do_dmeasure (SEXP object, SEXP y, SEXP x, SEXP times, SEXP params, SEXP log, SEXP gnsi)
{
 
  pompfunmode mode = undef;
  int ntimes, nvars, npars, ncovars, nreps, nrepsx, nrepsp, nobs;
  SEXP Snames, Pnames, Cnames, Onames;
  SEXP cvec, pompfun;
  SEXP fn, args, ans;
  SEXP F;
  int *dim;
  lookup_table_t covariate_table;
  double *cov;
 
  PROTECT(times = AS_NUMERIC(times));
  ntimes = length(times);
  if (ntimes < 1) err("length('times') = 0, no work to do.");
 
  PROTECT(y = as_matrix(y));
  dim = INTEGER(GET_DIM(y));
  nobs = dim[0];
 
  if (ntimes != dim[1])
    err("length of 'times' and 2nd dimension of 'y' do not agree.");
 
  PROTECT(x = as_state_array(x));
  dim = INTEGER(GET_DIM(x));
  nvars = dim[0]; nrepsx = dim[1];
 
  if (ntimes != dim[2])
    err("length of 'times' and 3rd dimension of 'x' do not agree.");
 
  PROTECT(params = as_matrix(params));
  dim = INTEGER(GET_DIM(params));
  npars = dim[0]; nrepsp = dim[1];
 
  nreps = (nrepsp > nrepsx) ? nrepsp : nrepsx;
 
  if ((nreps % nrepsp != 0) || (nreps % nrepsx != 0))
    err("larger number of replicates is not a multiple of smaller.");
 
  PROTECT(Onames = GET_ROWNAMES(GET_DIMNAMES(y)));
  PROTECT(Snames = GET_ROWNAMES(GET_DIMNAMES(x)));
  PROTECT(Pnames = GET_ROWNAMES(GET_DIMNAMES(params)));
  PROTECT(Cnames = get_covariate_names(GET_SLOT(object,install("covar"))));
 
  // set up the covariate table
  covariate_table = make_covariate_table(GET_SLOT(object,install("covar")),&ncovars);
  PROTECT(cvec = NEW_NUMERIC(ncovars));
  cov = REAL(cvec);
 
  // extract the user-defined function
  PROTECT(pompfun = GET_SLOT(object,install("dmeasure")));
  PROTECT(fn = pomp_fun_handler(pompfun,gnsi,&mode,Snames,Pnames,Onames,Cnames));
 
  // extract 'userdata' as pairlist
  PROTECT(args = GET_SLOT(object,install("userdata")));
 
  // create array to store results
  PROTECT(F = ret_array(nreps,ntimes));
 
  int nprotect = 13;
 
  switch (mode) {
 
  case Rfun: {
 
    double *ys = REAL(y), *xs = REAL(x), *ps = REAL(params), *time = REAL(times);
    double *ft = REAL(F);
    int j, k;
 
    // build argument list
    PROTECT(args = add_args(args,Onames,Snames,Pnames,Cnames,log)); nprotect++;
 
    for (k = 0; k < ntimes; k++, time++, ys += nobs) { // loop over times
 
      R_CheckUserInterrupt();   // check for user interrupt
 
      table_lookup(&covariate_table,*time,cov); // interpolate the covariates
 
      for (j = 0; j < nreps; j++, ft++) { // loop over replicates
 
        // evaluate the call
        PROTECT(
                ans = eval_call(
                                fn,args,
                                time,
                                ys,nobs,
                                xs+nvars*((j%nrepsx)+nrepsx*k),nvars,
                                ps+npars*(j%nrepsp),npars,
                                cov,ncovars
                                )
                );
 
        if (k == 0 && j == 0 && LENGTH(ans) != 1)
          err("user 'dmeasure' returns a vector of length %d when it should return a scalar.",LENGTH(ans));
 
        *ft = *(REAL(AS_NUMERIC(ans)));
 
        UNPROTECT(1);
 
      }
    }
  }
 
    break;
 
  case native: case regNative: {
    int *oidx, *sidx, *pidx, *cidx;
    int give_log;
    pomp_dmeasure *ff = NULL;
    double *yp = REAL(y), *xs = REAL(x), *ps = REAL(params), *time = REAL(times);
    double *ft = REAL(F);
    double *xp, *pp;
    int j, k;
 
    // extract state, parameter, covariate, observable indices
    sidx = INTEGER(GET_SLOT(pompfun,install("stateindex")));
    pidx = INTEGER(GET_SLOT(pompfun,install("paramindex")));
    oidx = INTEGER(GET_SLOT(pompfun,install("obsindex")));
    cidx = INTEGER(GET_SLOT(pompfun,install("covarindex")));
 
    give_log = *(INTEGER(AS_INTEGER(log)));
 
    // address of native routine
    *((void **) (&ff)) = R_ExternalPtrAddr(fn);
 
    for (k = 0; k < ntimes; k++, time++, yp += nobs) { // loop over times
 
      R_CheckUserInterrupt();   // check for user interrupt
 
      // interpolate the covar functions for the covariates
      table_lookup(&covariate_table,*time,cov);
 
      for (j = 0; j < nreps; j++, ft++) { // loop over replicates
 
        xp = &xs[nvars*((j%nrepsx)+nrepsx*k)];
        pp = &ps[npars*(j%nrepsp)];
 
        (*ff)(ft,yp,xp,pp,give_log,oidx,sidx,pidx,cidx,cov,*time);
 
      }
    }
 
  }
 
    break;
 
  default: {
    double *ft = REAL(F);
    int j, k;
 
    for (k = 0; k < ntimes; k++) { // loop over times
      for (j = 0; j < nreps; j++, ft++) { // loop over replicates
        *ft = R_NaReal;
      }
    }
 
    warn("'dmeasure' unspecified: likelihood undefined.");
 
  }
 
  }
 
  UNPROTECT(nprotect);
  return F;
}
SEXP do_dmeasure (SEXP object, SEXP y, SEXP x, SEXP times, SEXP params, SEXP log, SEXP gnsi) {…}