skeleton.c File Reference

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

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Functions
SEXP	add_skel_args (SEXP args, SEXP Snames, SEXP Pnames, SEXP Cnames)
static R_INLINE SEXP	eval_call (SEXP fn, SEXP args, double *t, double *x, int nvar, double *p, int npar, double *c, int ncov)
static R_INLINE SEXP	ret_array (int nvars, int nreps, int ntimes, SEXP Snames)
void	eval_skeleton_R (double *f, double *time, double *x, double *p, SEXP fn, SEXP args, SEXP Snames, int nvars, int npars, int ncovars, int ntimes, int nrepx, int nrepp, int nreps, lookup_table_t *covar_table, double *cov)
void	iterate_skeleton_R (double *X, double t, double deltat, double *time, double *x, double *p, SEXP fn, SEXP args, SEXP Snames, int nvars, int npars, int ncovars, int ntimes, int nrepp, int nreps, int nzeros, lookup_table_t *covar_table, int *zeroindex, double *cov)
void	eval_skeleton_native (double *f, double *time, double *x, double *p, int nvars, int npars, int ncovars, int ntimes, int nrepx, int nrepp, int nreps, int *sidx, int *pidx, int *cidx, lookup_table_t *covar_table, pomp_skeleton *fun, SEXP args, double *cov)
void	iterate_skeleton_native (double *X, double t, double deltat, double *time, double *x, double *p, int nvars, int npars, int ncovars, int ntimes, int nrepp, int nreps, int nzeros, int *sidx, int *pidx, int *cidx, lookup_table_t *covar_table, int *zeroindex, pomp_skeleton *fun, SEXP args, double *cov)
SEXP	do_skeleton (SEXP object, SEXP x, SEXP t, SEXP params, SEXP gnsi)

Function Documentation

add_skel_args()

SEXP add_skel_args	(	SEXP	args,
		SEXP	Snames,
		SEXP	Pnames,
		SEXP	Cnames
	)

Definition at line 10 of file skeleton.c.

{
 
  SEXP var;
  int v;
 
  PROTECT(args = VectorToPairList(args));
 
  // 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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do_skeleton()

SEXP do_skeleton	(	SEXP	object,
		SEXP	x,
		SEXP	t,
		SEXP	params,
		SEXP	gnsi
	)

Definition at line 326 of file skeleton.c.

{
 
  int nvars, npars, nrepp, nrepx, nreps, ntimes, ncovars;
  pompfunmode mode = undef;
  int *dim;
  SEXP Snames, Cnames, Pnames;
  SEXP pompfun, cov, ob;
  SEXP fn, args, F;
  lookup_table_t covariate_table;
 
  PROTECT(t = AS_NUMERIC(t));
  ntimes = LENGTH(t);
 
  PROTECT(x = as_state_array(x));
  dim = INTEGER(GET_DIM(x));
  nvars = dim[0]; nrepx = 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]; nrepp = dim[1];
 
  // 2nd dimension of 'x' and 'params' need not agree
  nreps = (nrepp > nrepx) ? nrepp : nrepx;
  if ((nreps % nrepp != 0) || (nreps % nrepx != 0))
    err("2nd dimensions of 'x' and 'params' are incompatible");
 
  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(cov = NEW_NUMERIC(ncovars));
 
  // extract the user-defined function
  PROTECT(ob = GET_SLOT(object,install("skeleton")));
  PROTECT(pompfun = GET_SLOT(ob,install("skel.fn")));
  PROTECT(fn = pomp_fun_handler(pompfun,gnsi,&mode,Snames,Pnames,NA_STRING,Cnames));
 
  // extract 'userdata' as pairlist
  PROTECT(args = GET_SLOT(object,install("userdata")));
 
  PROTECT(F = ret_array(nvars,nreps,ntimes,Snames));
 
  int nprotect = 12;
 
  switch (mode) {
 
  case Rfun: {
 
    PROTECT(args = add_skel_args(args,Snames,Pnames,Cnames)); nprotect++;
 
    eval_skeleton_R(REAL(F),REAL(t),REAL(x),REAL(params),
                    fn,args,Snames,
                    nvars,npars,ncovars,ntimes,nrepx,nrepp,nreps,
                    &covariate_table,REAL(cov));
 
  }
 
    break;
 
  case native: case regNative: {
    int *sidx, *pidx, *cidx;
    pomp_skeleton *ff = NULL;
 
    sidx = INTEGER(GET_SLOT(pompfun,install("stateindex")));
    pidx = INTEGER(GET_SLOT(pompfun,install("paramindex")));
    cidx = INTEGER(GET_SLOT(pompfun,install("covarindex")));
 
    *((void **) (&ff)) = R_ExternalPtrAddr(fn);
 
    eval_skeleton_native(
                         REAL(F),REAL(t),REAL(x),REAL(params),
                         nvars,npars,ncovars,ntimes,nrepx,nrepp,nreps,
                         sidx,pidx,cidx,&covariate_table,ff,args,REAL(cov));
 
  }
 
    break;
 
  default: {
 
    double *ft = REAL(F);
    int i, n = nvars*nreps*ntimes;
    for (i = 0; i < n; i++, ft++) *ft = R_NaReal;
    warn("'skeleton' unspecified: NAs generated.");
 
  }
 
  }
 
  UNPROTECT(nprotect);
  return F;
}

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eval_call()

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

static

Definition at line 57 of file skeleton.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;
 
  PROTECT(ob = LCONS(fn,args));
  PROTECT(ans = eval(ob,R_ClosureEnv(fn)));
 
  UNPROTECT(2);
  return ans;
 
}

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eval_skeleton_native()

void eval_skeleton_native	(	double *	f,
		double *	time,
		double *	x,
		double *	p,
		int	nvars,
		int	npars,
		int	ncovars,
		int	ntimes,
		int	nrepx,
		int	nrepp,
		int	nreps,
		int *	sidx,
		int *	pidx,
		int *	cidx,
		lookup_table_t *	covar_table,
		pomp_skeleton *	fun,
		SEXP	args,
		double *	cov
	)

Definition at line 245 of file skeleton.c.

{
  double *xp, *pp;
  int j, k;
 
  for (k = 0; k < ntimes; k++, time++) {
 
    R_CheckUserInterrupt();
 
    table_lookup(covar_table,*time,cov);
 
    for (j = 0; j < nreps; j++, f += nvars) {
 
      xp = &x[nvars*((j%nrepx)+nrepx*k)];
      pp = &p[npars*(j%nrepp)];
 
      (*fun)(f,xp,pp,sidx,pidx,cidx,cov,*time);
 
    }
  }
 
}

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eval_skeleton_R()

void eval_skeleton_R	(	double *	f,
		double *	time,
		double *	x,
		double *	p,
		SEXP	fn,
		SEXP	args,
		SEXP	Snames,
		int	nvars,
		int	npars,
		int	ncovars,
		int	ntimes,
		int	nrepx,
		int	nrepp,
		int	nreps,
		lookup_table_t *	covar_table,
		double *	cov
	)

Definition at line 93 of file skeleton.c.

   {
 
  SEXP ans, nm;
  double *fs;
  int *posn = 0;
  int i, j, k;
  int first = 1;
  int nprotect = 0;
 
  for (k = 0; k < ntimes; k++, time++) {
 
    R_CheckUserInterrupt();
 
    // interpolate the covar functions for the covariates
    table_lookup(covar_table,*time,cov);
 
    for (j = 0; j < nreps; j++, f += nvars) {
 
      if (first) {
 
        PROTECT(ans = eval_call(fn,args,time,
                                x+nvars*((j%nrepx)+nrepx*k),nvars,
                                p+npars*(j%nrepp),npars,
                                cov,ncovars));
 
        if (LENGTH(ans)!=nvars)
          err("'skeleton' returns a vector of %d state variables but %d are expected.",LENGTH(ans),nvars);
 
        // get name information to fix alignment problems
        PROTECT(nm = GET_NAMES(ans));
        if (invalid_names(nm))
          err("'skeleton' must return a named numeric vector.");
        posn = INTEGER(PROTECT(matchnames(Snames,nm,"state variables")));
 
        fs = REAL(AS_NUMERIC(ans));
        for (i = 0; i < nvars; i++) f[posn[i]] = fs[i];
 
        nprotect += 3;
        first = 0;
 
      } else {
 
        PROTECT(ans = eval_call(fn,args,time,
                                x+nvars*((j%nrepx)+nrepx*k),nvars,
                                p+npars*(j%nrepp),npars,
                                cov,ncovars));
 
        fs = REAL(AS_NUMERIC(ans));
        for (i = 0; i < nvars; i++) f[posn[i]] = fs[i];
 
        UNPROTECT(1);
 
      }
 
    }
  }
 
  UNPROTECT(nprotect);
 
}

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iterate_skeleton_native()

void iterate_skeleton_native	(	double *	X,
		double	t,
		double	deltat,
		double *	time,
		double *	x,
		double *	p,
		int	nvars,
		int	npars,
		int	ncovars,
		int	ntimes,
		int	nrepp,
		int	nreps,
		int	nzeros,
		int *	sidx,
		int *	pidx,
		int *	cidx,
		lookup_table_t *	covar_table,
		int *	zeroindex,
		pomp_skeleton *	fun,
		SEXP	args,
		double *	cov
	)

Definition at line 274 of file skeleton.c.

{
  int nsteps;
  double *xs, *Xs;
  int h, i, j, k;
 
  for (k = 0; k < ntimes; k++, time++, X += nvars*nreps) {
 
    R_CheckUserInterrupt();
 
    // compute number of steps needed
    nsteps = num_map_steps(t,*time,deltat);
 
    // set accumulator variables to zero
    for (i = 0; i < nzeros; i++)
      for (j = 0, xs = &x[zeroindex[i]]; j < nreps; j++, xs += nvars)
        *xs = 0.0;
 
    for (h = 0; h < nsteps; h++) {
 
      // interpolate the covariates
      table_lookup(covar_table,t,cov);
 
      for (j = 0, Xs = X, xs = x; j < nreps; j++, Xs += nvars, xs += nvars) {
 
        (*fun)(Xs,xs,p+npars*(j%nrepp),sidx,pidx,cidx,cov,t);
 
      }
 
      memcpy(x,X,nvars*nreps*sizeof(double));
 
      if (h != nsteps-1) {
        t += deltat;
      } else {
        t = *time;
      }
 
    }
 
    if (nsteps == 0) memcpy(X,x,nvars*nreps*sizeof(double));
 
  }
 
}

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iterate_skeleton_R()

void iterate_skeleton_R	(	double *	X,
		double	t,
		double	deltat,
		double *	time,
		double *	x,
		double *	p,
		SEXP	fn,
		SEXP	args,
		SEXP	Snames,
		int	nvars,
		int	npars,
		int	ncovars,
		int	ntimes,
		int	nrepp,
		int	nreps,
		int	nzeros,
		lookup_table_t *	covar_table,
		int *	zeroindex,
		double *	cov
	)

Definition at line 161 of file skeleton.c.

{
 
  SEXP ans, nm;
  double *ap, *xs;
  int nsteps;
  int *posn = 0;
  int h, i, j, k;
  int first = 1;
  int nprotect = 0;
 
  for (k = 0; k < ntimes; k++, time++, X += nvars*nreps) {
 
    R_CheckUserInterrupt();
 
    // compute number of steps needed
    nsteps = num_map_steps(t,*time,deltat);
 
    // set accumulator variables to zero
    for (i = 0; i < nzeros; i++)
      for (j = 0, xs = &x[zeroindex[i]]; j < nreps; j++, xs += nvars)
        *xs = 0.0;
 
    for (h = 0; h < nsteps; h++) {
 
      // interpolate the covariates
      table_lookup(covar_table,t,cov);
 
      for (j = 0, xs = x; j < nreps; j++, xs += nvars) {
 
        if (first) {
 
          PROTECT(ans = eval_call(fn,args,&t,xs,nvars,p+npars*(j%nrepp),npars,cov,ncovars));
 
          if (LENGTH(ans) != nvars)
            err("'skeleton' returns a vector of %d state variables but %d are expected.",LENGTH(ans),nvars);
 
          // get name information to fix alignment problems
          PROTECT(nm = GET_NAMES(ans));
          if (invalid_names(nm)) err("'skeleton' must return a named numeric vector.");
          posn = INTEGER(PROTECT(matchnames(Snames,nm,"state variables")));
 
          ap = REAL(AS_NUMERIC(ans));
          for (i = 0; i < nvars; i++) xs[posn[i]] = ap[i];
 
          nprotect += 3;
          first = 0;
 
        } else {
 
          PROTECT(ans = eval_call(fn,args,&t,xs,nvars,p+npars*(j%nrepp),npars,cov,ncovars));
 
          ap = REAL(AS_NUMERIC(ans));
          for (i = 0; i < nvars; i++) xs[posn[i]] = ap[i];
 
          UNPROTECT(1);
 
        }
 
      }
 
      if (h != nsteps-1) {
        t += deltat;
      } else {
        t = *time;
      }
 
    }
 
    memcpy(X,x,nvars*nreps*sizeof(double));
 
  }
 
  UNPROTECT(nprotect);
 
}

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ret_array()

static R_INLINE SEXP ret_array ( int  nvars, int  nreps, int  ntimes, SEXP  Snames  )

static

Definition at line 81 of file skeleton.c.

{
  SEXP X;
  int dim[3] = {nvars, nreps, ntimes};
  const char *dimnms[3] = {"name",".id","time"};
  PROTECT(X = makearray(3,dim));
  setrownames(X,Snames,3);
  fixdimnames(X,dimnms,3);
  UNPROTECT(1);
  return X;
}

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