euler.c File Reference

#include <R.h>
#include <Rmath.h>
#include <Rdefines.h>
#include "internal.h"

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Functions
static R_INLINE SEXP	add_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP Cnames)
static R_INLINE SEXP	eval_call (SEXP fn, SEXP args, double *t, double *dt, double *x, int nvar, double *p, int npar, double *c, int ncov)
static R_INLINE SEXP	ret_array (int n, int nreps, int ntimes, SEXP names)
SEXP	euler_simulator (SEXP func, SEXP xstart, SEXP tstart, SEXP times, SEXP params, double deltat, rprocmode method, SEXP accumvars, SEXP covar, SEXP args, SEXP gnsi)
int	num_euler_steps (double t1, double t2, double *deltat)
int	num_map_steps (double t1, double t2, double deltat)

Function Documentation

add_args()

static R_INLINE SEXP add_args ( SEXP  args, SEXP  Snames, SEXP  Pnames, SEXP  Cnames  )

static

Definition at line 10 of file euler.c.

{
 
  SEXP var;
  int v;
 
  PROTECT(args = VectorToPairList(args));
 
  // we construct the call from end to beginning
  // delta.t, covariates, parameter, states, then time
 
  // 'delta.t'
  var = NEW_NUMERIC(1);
  args = LCONS(var,args);
  UNPROTECT(1);
  PROTECT(args);
  SET_TAG(args,install("delta.t"));
 
  // 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)));
  }
 
  // Time
  var = NEW_NUMERIC(1);
  args = LCONS(var,args);
  UNPROTECT(1);
  PROTECT(args);
  SET_TAG(args,install("t"));
 
  UNPROTECT(1);
  return args;
 
}

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euler_simulator()

SEXP euler_simulator	(	SEXP	func,
		SEXP	xstart,
		SEXP	tstart,
		SEXP	times,
		SEXP	params,
		double	deltat,
		rprocmode	method,
		SEXP	accumvars,
		SEXP	covar,
		SEXP	args,
		SEXP	gnsi
	)

Definition at line 107 of file euler.c.

   {
 
  pompfunmode mode = undef;
  int nvars, npars, nreps, ntimes, nzeros, ncovars;
  double *cov, t0;
  SEXP cvec, X, fn;
 
  if (deltat <= 0) err("'delta.t' should be a positive number."); // #nocov
 
  int *dim;
  dim = INTEGER(GET_DIM(xstart)); nvars = dim[0]; nreps = dim[1];
  dim = INTEGER(GET_DIM(params)); npars = dim[0];
  ntimes = LENGTH(times);
 
  PROTECT(tstart = AS_NUMERIC(tstart));
  PROTECT(times = AS_NUMERIC(times));
  t0 = *(REAL(tstart));
  if (t0 > *(REAL(times))) err("'t0' must be no later than 'times[1]'.");
 
  SEXP Snames, Pnames, Cnames;
  PROTECT(Snames = GET_ROWNAMES(GET_DIMNAMES(xstart)));
  PROTECT(Pnames = GET_ROWNAMES(GET_DIMNAMES(params)));
  PROTECT(Cnames = get_covariate_names(covar));
 
  // set up the covariate table
  lookup_table_t covariate_table = make_covariate_table(covar,&ncovars);
  PROTECT(cvec = NEW_NUMERIC(ncovars));
  cov = REAL(cvec);
 
  // indices of accumulator variables
  nzeros = LENGTH(accumvars);
  int *zidx = INTEGER(PROTECT(matchnames(Snames,accumvars,"state variables")));
 
  // extract user function
  PROTECT(fn = pomp_fun_handler(func,gnsi,&mode,Snames,Pnames,NA_STRING,Cnames));
 
  // array to hold results
  PROTECT(X = ret_array(nvars,nreps,ntimes,Snames));
 
  // copy the start values into the result array
  memcpy(REAL(X),REAL(xstart),nvars*nreps*sizeof(double));
 
  // set up
 
  int nprotect = 9;
  int *pidx = 0, *sidx = 0, *cidx = 0;
  pomp_onestep_sim *ff = NULL;
 
  switch (mode) {
 
  case Rfun:
    // construct list of all arguments
    PROTECT(args = add_args(args,Snames,Pnames,Cnames)); nprotect++;
    break;
 
  case native: case regNative:
    // construct state, parameter, covariate indices
    sidx = INTEGER(GET_SLOT(func,install("stateindex")));
    pidx = INTEGER(GET_SLOT(func,install("paramindex")));
    cidx = INTEGER(GET_SLOT(func,install("covarindex")));
 
    *((void **) (&ff)) = R_ExternalPtrAddr(fn);
 
    GetRNGstate();
    break;
 
  default: // #nocov
    err("unrecognized 'mode' %d",mode); // #nocov
    break;                              // #nocov
  }
 
  // main computation loop
  int step;
  double *xt, *time, t;
  int first = 1;
 
  for (
       step = 0, xt = REAL(X), time = REAL(times), t = t0;
       step < ntimes;
       step++, xt += nvars*nreps
       ) {
 
    double dt;
    int nstep = 0;
    int i, j, k;
 
    R_CheckUserInterrupt();
 
    if (t > time[step]) err("'times' must be an increasing sequence.");  // #nocov
 
    // set accumulator variables to zero
    for (j = 0; j < nreps; j++)
      for (i = 0; i < nzeros; i++)
        xt[zidx[i]+nvars*j] = 0.0;
 
    // determine size and number of time-steps
    switch (method) {
    case onestep: default:      // one step
      dt = time[step]-t;
      nstep = 1;
      break;
    case discrete:              // fixed step
      dt = deltat;
      nstep = num_map_steps(t,time[step],dt);
      break;
    case euler:                 // Euler method
      dt = deltat;
      nstep = num_euler_steps(t,time[step],&dt);
      break;
    }
 
    // loop over individual steps
    for (k = 0; k < nstep; k++) {
 
      // interpolate the covar functions for the covariates
      table_lookup(&covariate_table,t,cov);
 
      // loop over replicates
      double *ap, *pm, *xm, *ps = REAL(params);
 
      for (j = 0, pm = ps, xm = xt; j < nreps; j++, pm += npars, xm += nvars) {
 
        switch (mode) {
 
        case Rfun:
          {
            SEXP ans, nm;
 
            if (first) {
 
              PROTECT(ans = eval_call(fn,args,&t,&dt,xm,nvars,pm,npars,cov,ncovars));
 
              PROTECT(nm = GET_NAMES(ans));
              if (invalid_names(nm))
                err("'rprocess' must return a named numeric vector.");
              pidx = INTEGER(PROTECT(matchnames(nm,Snames,"state variables")));
 
              nprotect += 3;
 
              ap = REAL(AS_NUMERIC(ans));
              for (i = 0; i < nvars; i++) xm[pidx[i]] = ap[i];
 
              first = 0;
 
            } else {
 
              PROTECT(ans = eval_call(fn,args,&t,&dt,xm,nvars,pm,npars,cov,ncovars));
 
              ap = REAL(AS_NUMERIC(ans));
              for (i = 0; i < nvars; i++) xm[pidx[i]] = ap[i];
 
              UNPROTECT(1);
 
            }
          }
          break;
 
        case native: case regNative:
          (*ff)(xm,pm,sidx,pidx,cidx,cov,t,dt);
          break;
 
        default:                              // #nocov
          err("unrecognized 'mode' %d",mode); // #nocov
          break;                              // #nocov
 
        }
 
      }
 
      t += dt;
 
      if ((method == euler) && (k == nstep-2)) { // penultimate step
        dt = time[step]-t;
        t = time[step]-dt;
      }
 
    }
 
    if (step < ntimes-1)
      memcpy(xt+nvars*nreps,xt,nreps*nvars*sizeof(double));
 
  }
 
  // clean up
  switch (mode) {
 
  case native: case regNative: {
 
    PutRNGstate();
 
  }
 
    break;
 
  case Rfun: default:
 
    break;
 
  }
 
  UNPROTECT(nprotect);
  return X;
 
}

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eval_call()

static R_INLINE SEXP eval_call ( SEXP  fn, SEXP  args, double *  t, double *  dt, double *  x, int  nvar, double *  p, int  npar, double *  c, int  ncov  )

static

Definition at line 67 of file euler.c.

{
 
  SEXP var = args, ans, ob;
  int v;
 
  *(REAL(CAR(var))) = *t; var = CDR(var);
  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;
  *(REAL(CAR(var))) = *dt; var = CDR(var);
 
  PROTECT(ob = LCONS(fn,args));
  PROTECT(ans = eval(ob,CLOENV(fn)));
 
  UNPROTECT(2);
  return ans;
 
}

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num_euler_steps()

int num_euler_steps	(	double	t1,
		double	t2,
		double *	deltat
	)

Definition at line 317 of file euler.c.

                                                           {
  double tol = sqrt(DBL_EPSILON);
  int nstep;
  // nstep will be the number of Euler steps to take in going from t1 to t2.
  // note also that the stepsize changes.
  // this choice is meant to be conservative
  // (i.e., so that the actual deltat does not exceed the specified deltat
  // by more than the relative tolerance 'tol')
  // and to counteract roundoff error.
  // It seems to work well, but is not guaranteed:
  // suggestions would be appreciated.
 
  if (t1 >= t2) {
    *deltat = 0.0;
    nstep = 0;
  } else if (t1+*deltat >= t2) {
    *deltat = t2-t1;
    nstep = 1;
  } else {
    nstep = (int) ceil((t2-t1)/(*deltat)/(1+tol));
    *deltat = (t2-t1)/((double) nstep);
  }
  return nstep;
}

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num_map_steps()

int num_map_steps	(	double	t1,
		double	t2,
		double	deltat
	)

Definition at line 342 of file euler.c.

                                                        {
  double tol = sqrt(DBL_EPSILON);
  int nstep;
  // nstep will be the number of discrete-time steps to take in going from t1 to t2.
  nstep = (int) floor((t2-t1)/deltat/(1-tol));
  return (nstep > 0) ? nstep : 0;
}

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ret_array()

static R_INLINE SEXP ret_array ( int  n, int  nreps, int  ntimes, SEXP  names  )

static

Definition at line 92 of file euler.c.

{
  int dim[3] = {n, nreps, ntimes};
  const char *dimnm[3] = {"name", ".id", "time"};
  SEXP Y;
 
  PROTECT(Y = makearray(3,dim));
  setrownames(Y,names,3);
  fixdimnames(Y,dimnm,3);
 
  UNPROTECT(1);
  return Y;
 
}

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