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

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Data Structures
struct	lookup_table_t

Macros
#define	MATCHROWNAMES(X, N, W) (matchnames(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(W)))

#define	MATCHCOLNAMES(X, N, W) (matchnames(GET_COLNAMES(GET_DIMNAMES(X)),(N),(W)))

Typedefs
typedef SEXP	pomp_fun_handler_t(SEXP pfun, SEXP gnsi, pompfunmode *mode, SEXP S, SEXP P, SEXP O, SEXP C)

typedef SEXP	load_stack_incr_t(SEXP pack)

typedef SEXP	load_stack_decr_t(SEXP pack)

typedef lookup_table_t	make_covariate_table_t(SEXP object, int *ncovar)

typedef void	table_lookup_t(lookup_table_t tab, double x, double y)

typedef SEXP	apply_probe_data_t(SEXP object, SEXP probes)

typedef SEXP	apply_probe_sim_t(SEXP object, SEXP nsim, SEXP params, SEXP probes, SEXP datval, SEXP gnsi)

typedef SEXP	systematic_resampling_t(SEXP weights)

typedef void	set_pomp_userdata_t(SEXP userdata)

typedef void	unset_pomp_userdata_t(void)

typedef SEXP	get_covariate_names_t(SEXP object)

Enumerations
enum	pompfunmode { undef =0 , Rfun =1 , native =2 , regNative =3 }

enum	rprocmode { dflt =0 , onestep =1 , discrete =2 , euler =3 , gill =4 }

Functions
static R_INLINE SEXP	makearray (int rank, const int *dim)

static R_INLINE int	invalid_names (SEXP names)

static R_INLINE SEXP	matchnames (SEXP provided, SEXP needed, const char *where)

static R_INLINE void	fillrownames (SEXP x, SEXP names)

static R_INLINE void	setrownames (SEXP x, SEXP names, int rank)

static R_INLINE void	setcolnames (SEXP x, SEXP names)

static R_INLINE void	fixdimnames (SEXP x, const char **names, int n)

static R_INLINE SEXP	as_matrix (SEXP x)

static R_INLINE SEXP	as_state_array (SEXP x)

static R_INLINE SEXP	getListElement (SEXP list, const char *str)

static R_INLINE SEXP	getPairListElement (SEXP list, const char *name)

Macro Definition Documentation

◆ MATCHCOLNAMES

#define MATCHCOLNAMES	(	X,
		N,
		W
	)	(matchnames(GET_COLNAMES(GET_DIMNAMES(X)),(N),(W)))

Definition at line 14 of file pomp_defines.h.

◆ MATCHROWNAMES

#define MATCHROWNAMES	(	X,
		N,
		W
	)	(matchnames(GET_ROWNAMES(GET_DIMNAMES(X)),(N),(W)))

Definition at line 13 of file pomp_defines.h.

Typedef Documentation

◆ apply_probe_data_t

typedef SEXP apply_probe_data_t(SEXP object, SEXP probes)

Definition at line 33 of file pomp_defines.h.

◆ apply_probe_sim_t

typedef SEXP apply_probe_sim_t(SEXP object, SEXP nsim, SEXP params, SEXP probes, SEXP datval, SEXP gnsi)

Definition at line 34 of file pomp_defines.h.

◆ get_covariate_names_t

typedef SEXP get_covariate_names_t(SEXP object)

Definition at line 38 of file pomp_defines.h.

◆ load_stack_decr_t

typedef SEXP load_stack_decr_t(SEXP pack)

Definition at line 30 of file pomp_defines.h.

◆ load_stack_incr_t

typedef SEXP load_stack_incr_t(SEXP pack)

Definition at line 29 of file pomp_defines.h.

◆ make_covariate_table_t

typedef lookup_table_t make_covariate_table_t(SEXP object, int *ncovar)

Definition at line 31 of file pomp_defines.h.

◆ pomp_fun_handler_t

typedef SEXP pomp_fun_handler_t(SEXP pfun, SEXP gnsi, pompfunmode *mode, SEXP S, SEXP P, SEXP O, SEXP C)

Definition at line 28 of file pomp_defines.h.

◆ set_pomp_userdata_t

typedef void set_pomp_userdata_t(SEXP userdata)

Definition at line 36 of file pomp_defines.h.

◆ systematic_resampling_t

typedef SEXP systematic_resampling_t(SEXP weights)

Definition at line 35 of file pomp_defines.h.

◆ table_lookup_t

typedef void table_lookup_t(lookup_table_t *tab, double x, double *y)

Definition at line 32 of file pomp_defines.h.

◆ unset_pomp_userdata_t

typedef void unset_pomp_userdata_t(void)

Definition at line 37 of file pomp_defines.h.

Enumeration Type Documentation

◆ pompfunmode

enum pompfunmode

Enumerator
undef
Rfun
native
regNative

Definition at line 16 of file pomp_defines.h.

16{undef=0,Rfun=1,native=2,regNative=3} pompfunmode;

pompfunmode

Definition pomp_defines.h:16

Rfun

@ Rfun

Definition pomp_defines.h:16

native

@ native

Definition pomp_defines.h:16

undef

@ undef

Definition pomp_defines.h:16

regNative

@ regNative

Definition pomp_defines.h:16

◆ rprocmode

enum rprocmode

Enumerator
dflt
onestep
discrete
euler
gill

Definition at line 17 of file pomp_defines.h.

17{dflt=0,onestep=1,discrete=2,euler=3,gill=4} rprocmode;

rprocmode

Definition pomp_defines.h:17

gill

@ gill

Definition pomp_defines.h:17

discrete

@ discrete

Definition pomp_defines.h:17

dflt

@ dflt

Definition pomp_defines.h:17

onestep

@ onestep

Definition pomp_defines.h:17

euler

@ euler

Definition pomp_defines.h:17

Function Documentation

◆ as_matrix()

static R_INLINE SEXP as_matrix ( SEXP x )

static

Definition at line 145 of file pomp_defines.h.

                                        {
  int nprotect = 1;
  SEXP dim, names;
  int *xdim, nrow, ncol;
  PROTECT(dim = GET_DIM(x));
  if (isNull(dim)) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_NAMES(x));
    nprotect += 2;
    dim = NEW_INTEGER(2);
    xdim = INTEGER(dim); xdim[0] = LENGTH(x); xdim[1] = 1;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,2);
  } else if (LENGTH(dim) == 1) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_ROWNAMES(GET_DIMNAMES(x)));
    nprotect += 2;
    dim = NEW_INTEGER(2);
    xdim = INTEGER(dim); xdim[0] = LENGTH(x); xdim[1] = 1;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,2);
  } else if (LENGTH(dim) > 2) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_ROWNAMES(GET_DIMNAMES(x)));
    nprotect += 2;
    nrow = INTEGER(dim)[0]; ncol = LENGTH(x)/nrow;
    dim = NEW_INTEGER(2);
    xdim = INTEGER(dim); xdim[0] = nrow; xdim[1] = ncol;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,2);
  }
  UNPROTECT(nprotect);
  return x;
}

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◆ as_state_array()

static R_INLINE SEXP as_state_array ( SEXP x )

static

Definition at line 183 of file pomp_defines.h.

                                             {
  int nprotect = 1;
  SEXP dim, names;
  int *xdim, nrow, ncol;
  PROTECT(dim = GET_DIM(x));
  if (isNull(dim)) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_NAMES(x));
    nprotect += 2;
    dim = NEW_INTEGER(3);
    xdim = INTEGER(dim); xdim[0] = LENGTH(x); xdim[1] = 1; xdim[2] = 1;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,3);
  } else if (LENGTH(dim) == 1) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_ROWNAMES(GET_DIMNAMES(x)));
    nprotect += 2;
    dim = NEW_INTEGER(3);
    xdim = INTEGER(dim); xdim[0] = LENGTH(x); xdim[1] = 1; xdim[2] = 1;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,3);
  } else if (LENGTH(dim) == 2) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_ROWNAMES(GET_DIMNAMES(x)));
    nprotect += 2;
    xdim = INTEGER(dim); nrow = xdim[0]; ncol = xdim[1];
    dim = NEW_INTEGER(3);
    xdim = INTEGER(dim); xdim[0] = nrow; xdim[1] = 1; xdim[2] = ncol;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,3);
  } else if (LENGTH(dim) > 3) {
    PROTECT(x = duplicate(x));
    PROTECT(names = GET_ROWNAMES(GET_DIMNAMES(x)));
    nprotect += 2;
    xdim = INTEGER(dim); nrow = xdim[0]; ncol = xdim[1];
    dim = NEW_INTEGER(3);
    xdim = INTEGER(dim);
    xdim[0] = nrow; xdim[1] = ncol; xdim[2] = LENGTH(x)/nrow/ncol;
    SET_DIM(x,dim);
    SET_NAMES(x,R_NilValue);
    setrownames(x,names,3);
  }
  UNPROTECT(nprotect);
  return x;
}

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◆ fillrownames()

static R_INLINE void fillrownames	(	SEXP	x,
		SEXP	names
	)

static

Definition at line 87 of file pomp_defines.h.

                                                       {
  SEXP dim, dimnms;
  int nr;
  PROTECT(names = AS_CHARACTER(names));
  PROTECT(dim = GET_DIM(x));
  PROTECT(dimnms = allocVector(VECSXP,length(dim)));
  nr = INTEGER(dim)[0];
  if (nr > length(names)) {
    SEXP nm;
    int k;
    PROTECT(nm = NEW_CHARACTER(nr));
    for (k = 0; k < length(names); k++) {
      SET_STRING_ELT(nm,k,STRING_ELT(names,k));
    }
    SET_ELEMENT(dimnms,0,nm);
    UNPROTECT(1);
  } else {
    SET_ELEMENT(dimnms,0,names);
  }
  SET_DIMNAMES(x,dimnms);
  UNPROTECT(3);
}

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◆ fixdimnames()

static R_INLINE void fixdimnames	(	SEXP	x,
		const char **	names,
		int	n
	)

static

Definition at line 129 of file pomp_defines.h.

                                                                     {
  int nprotect = 2;
  int i;
  SEXP dimnames, nm;
  PROTECT(dimnames = GET_DIMNAMES(x));
  if (isNull(dimnames)) {
    PROTECT(dimnames = allocVector(VECSXP,n)); nprotect++;
  }
  PROTECT(nm = allocVector(VECSXP,n));
  for (i = 0; i < n; i++)
    SET_ELEMENT(nm,i,mkChar(names[i]));
  SET_NAMES(dimnames,nm);
  SET_DIMNAMES(x,dimnames);
  UNPROTECT(nprotect);
}

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◆ getListElement()

static R_INLINE SEXP getListElement	(	SEXP	list,
		const char *	str
	)

static

Definition at line 232 of file pomp_defines.h.

{
  SEXP elmt = R_NilValue;
  SEXP names = getAttrib(list,R_NamesSymbol);
  for (R_len_t i = 0; i < length(list); i++)
    if (strcmp(CHAR(STRING_ELT(names,i)),str) == 0) {
      elmt = VECTOR_ELT(list,i);
      break;
    }
  return elmt;
}

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◆ getPairListElement()

static R_INLINE SEXP getPairListElement	(	SEXP	list,
		const char *	name
	)

static

Definition at line 244 of file pomp_defines.h.

{
  const char *tag;
  while (list != R_NilValue) {
    tag = CHAR(PRINTNAME(TAG(list)));
    if (strcmp(tag,name)==0) break;
    list = CDR(list);
  }
  return CAR(list);
}

◆ invalid_names()

static R_INLINE int invalid_names ( SEXP names )

static

Definition at line 55 of file pomp_defines.h.

                                               {
  return isNull(names);
}

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◆ makearray()

static R_INLINE SEXP makearray	(	int	rank,
		const int *	dim
	)

static

Definition at line 40 of file pomp_defines.h.

                                                          {
  int *dimp, k;
  double *xp;
  SEXP dimx, x;
  PROTECT(dimx = NEW_INTEGER(rank));
  dimp = INTEGER(dimx);
  for (k = 0; k < rank; k++) dimp[k] = dim[k];
  PROTECT(x = allocArray(REALSXP,dimx));
  xp = REAL(x);
  for (k = 0; k < length(x); k++) xp[k] = NA_REAL;
  UNPROTECT(2);
  return x;
}

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◆ matchnames()

static R_INLINE SEXP matchnames	(	SEXP	provided,
		SEXP	needed,
		const char *	where
	)

static

Definition at line 59 of file pomp_defines.h.

   {
  int m = LENGTH(provided);
  int n = length(needed);
  SEXP index;
  int *idx, i, j;
  PROTECT(provided = AS_CHARACTER(provided));
  PROTECT(needed = AS_CHARACTER(needed));
  if (invalid_names(provided))
    err("invalid variable names among the %s.",where); // #nocov
  PROTECT(index = NEW_INTEGER(n));
  idx = INTEGER(index);
  for (i = 0; i < n; i++) {
    for (j = 0; j < m; j++) {
      if (!strcmp(CHAR(STRING_ELT(provided,j)),CHAR(STRING_ELT(needed,i)))) {
        idx[i] = j;
        break;
      }
    }
    if (j==m)
      err("variable '%s' not found among the %s.",CHAR(STRING_ELT(needed,i)),where);
  }
  UNPROTECT(3);
  return index;
}

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◆ setcolnames()

static R_INLINE void setcolnames	(	SEXP	x,
		SEXP	names
	)

static

Definition at line 121 of file pomp_defines.h.

                                                      {
  SEXP dn;
  PROTECT(dn = GET_DIMNAMES(x));
  SET_ELEMENT(dn,1,names);
  SET_DIMNAMES(x,dn);
  UNPROTECT(1);
}

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◆ setrownames()

static R_INLINE void setrownames	(	SEXP	x,
		SEXP	names,
		int	rank
	)

static

Definition at line 110 of file pomp_defines.h.

                                                                {
  SEXP dimnms, nm;
  PROTECT(nm = AS_CHARACTER(names));
  PROTECT(dimnms = allocVector(VECSXP,rank));
  SET_ELEMENT(dimnms,0,nm);     // set row names
  SET_DIMNAMES(x,dimnms);
  UNPROTECT(2);
}

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Data Structures

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

◆ MATCHCOLNAMES

◆ MATCHROWNAMES

Typedef Documentation

◆ apply_probe_data_t

◆ apply_probe_sim_t

◆ get_covariate_names_t

◆ load_stack_decr_t

◆ load_stack_incr_t

◆ make_covariate_table_t

◆ pomp_fun_handler_t

◆ set_pomp_userdata_t

◆ systematic_resampling_t

◆ table_lookup_t

◆ unset_pomp_userdata_t

Enumeration Type Documentation

◆ pompfunmode

◆ rprocmode

Function Documentation

◆ as_matrix()

◆ as_state_array()

◆ fillrownames()

◆ fixdimnames()

◆ getListElement()

◆ getPairListElement()

◆ invalid_names()

◆ makearray()

◆ matchnames()

◆ setcolnames()

◆ setrownames()