static R_INLINE SEXP matchnames (SEXP x, SEXP names, const char *where) {
int nprotect = 0;
int n = length(names);
int *idx, k;
SEXP index, nm;
PROTECT(nm = AS_CHARACTER(names)); nprotect++;
PROTECT(index = match(x,names,0)); nprotect++;
idx = INTEGER(index);
for (k = 0; k < n; k++) {
if (idx[k]==0)
error("variable '%s' not found among the %s",
CHARACTER_DATA(STRING_ELT(nm,k)),
where);
idx[k] -= 1;
}
UNPROTECT(nprotect);
return index;
}
int
RS_XML(externalEntityHandler)(XML_Parser parser, const XML_Char *context,
const XML_Char *base, const XML_Char *systemId,
const XML_Char *publicId)
{
RS_XMLParserData *parserData = (RS_XMLParserData*)XML_GetUserData(parser);
USER_OBJECT_ opArgs;
int i, num;
const XML_Char *xml_args[4];
num = sizeof(xml_args)/sizeof(xml_args[0]);
xml_args[0] = context; xml_args[1] = base;xml_args[2] = systemId; xml_args[3] = publicId;
opArgs = NEW_LIST(num);
for(i =0;i < num; i++) {
RECURSIVE_DATA(opArgs)[i] = NEW_CHARACTER(1);
CHARACTER_DATA(RECURSIVE_DATA(opArgs)[i])[0] = ENC_COPY_TO_USER_STRING(xml_args[i] ? xml_args[i] : "");
}
RS_XML(callUserFunction)("externalEntity", NULL, parserData, opArgs);
return(1); /* ok to go on */
}
SEXP do_init_state (SEXP object, SEXP params, SEXP t0, SEXP nsim, SEXP gnsi)
{
int nprotect = 0;
SEXP Pnames, Snames;
SEXP x = R_NilValue;
int *dim;
int npar, nrep, nvar, ns;
int definit;
int xdim[2];
const char *dimnms[2] = {"variable","rep"};
ns = *(INTEGER(AS_INTEGER(nsim)));
PROTECT(params = as_matrix(params)); nprotect++;
PROTECT(Pnames = GET_ROWNAMES(GET_DIMNAMES(params))); nprotect++;
dim = INTEGER(GET_DIM(params));
npar = dim[0]; nrep = dim[1];
if (ns % nrep != 0)
errorcall(R_NilValue,"in 'init.state': number of desired state-vectors 'nsim' is not a multiple of ncol('params')");
definit = *(INTEGER(GET_SLOT(object,install("default.init"))));
if (definit) { // default initializer
SEXP fcall, pat, repl, val, ivpnames, statenames;
int *pidx, j, k;
double *xp, *pp;
PROTECT(pat = NEW_CHARACTER(1)); nprotect++;
SET_STRING_ELT(pat,0,mkChar("\\.0$"));
PROTECT(repl = NEW_CHARACTER(1)); nprotect++;
SET_STRING_ELT(repl,0,mkChar(""));
PROTECT(val = NEW_LOGICAL(1)); nprotect++;
*(INTEGER(val)) = 1;
// extract names of IVPs
PROTECT(fcall = LCONS(val,R_NilValue)); nprotect++;
SET_TAG(fcall,install("value"));
PROTECT(fcall = LCONS(Pnames,fcall)); nprotect++;
SET_TAG(fcall,install("x"));
PROTECT(fcall = LCONS(pat,fcall)); nprotect++;
SET_TAG(fcall,install("pattern"));
PROTECT(fcall = LCONS(install("grep"),fcall)); nprotect++;
PROTECT(ivpnames = eval(fcall,R_BaseEnv)); nprotect++;
nvar = LENGTH(ivpnames);
if (nvar < 1) {
errorcall(R_NilValue,"in default 'initializer': there are no parameters with suffix '.0'. See '?pomp'.");
}
pidx = INTEGER(PROTECT(match(Pnames,ivpnames,0))); nprotect++;
for (k = 0; k < nvar; k++) pidx[k]--;
// construct names of state variables
PROTECT(fcall = LCONS(ivpnames,R_NilValue)); nprotect++;
SET_TAG(fcall,install("x"));
PROTECT(fcall = LCONS(repl,fcall)); nprotect++;
SET_TAG(fcall,install("replacement"));
PROTECT(fcall = LCONS(pat,fcall)); nprotect++;
SET_TAG(fcall,install("pattern"));
PROTECT(fcall = LCONS(install("sub"),fcall)); nprotect++;
PROTECT(statenames = eval(fcall,R_BaseEnv)); nprotect++;
xdim[0] = nvar; xdim[1] = ns;
PROTECT(x = makearray(2,xdim)); nprotect++;
setrownames(x,statenames,2);
fixdimnames(x,dimnms,2);
for (j = 0, xp = REAL(x); j < ns; j++) {
pp = REAL(params) + npar*(j%nrep);
for (k = 0; k < nvar; k++, xp++)
*xp = pp[pidx[k]];
}
} else { // user-supplied initializer
SEXP pompfun, fcall, fn, tcovar, covar, covars = R_NilValue;
pompfunmode mode = undef;
double *cp = NULL;
// extract the initializer function and its environment
PROTECT(pompfun = GET_SLOT(object,install("initializer"))); nprotect++;
PROTECT(fn = pomp_fun_handler(pompfun,gnsi,&mode)); nprotect++;
// extract covariates and interpolate
PROTECT(tcovar = GET_SLOT(object,install("tcovar"))); nprotect++;
if (LENGTH(tcovar) > 0) { // do table lookup
PROTECT(covar = GET_SLOT(object,install("covar"))); nprotect++;
PROTECT(covars = lookup_in_table(tcovar,covar,t0)); nprotect++;
cp = REAL(covars);
}
// extract userdata
PROTECT(fcall = VectorToPairList(GET_SLOT(object,install("userdata")))); nprotect++;
switch (mode) {
case Rfun: // use R function
{
SEXP par, rho, x1, x2;
double *p, *pp, *xp, *xt;
int j, *midx;
// extract covariates and interpolate
if (LENGTH(tcovar) > 0) { // add covars to call
PROTECT(fcall = LCONS(covars,fcall)); nprotect++;
SET_TAG(fcall,install("covars"));
}
// parameter vector
PROTECT(par = NEW_NUMERIC(npar)); nprotect++;
SET_NAMES(par,Pnames);
pp = REAL(par);
// finish constructing the call
PROTECT(fcall = LCONS(t0,fcall)); nprotect++;
SET_TAG(fcall,install("t0"));
PROTECT(fcall = LCONS(par,fcall)); nprotect++;
SET_TAG(fcall,install("params"));
PROTECT(fcall = LCONS(fn,fcall)); nprotect++;
// evaluation environment
PROTECT(rho = (CLOENV(fn))); nprotect++;
p = REAL(params);
memcpy(pp,p,npar*sizeof(double)); // copy the parameters
PROTECT(x1 = eval(fcall,rho)); nprotect++; // do the call
PROTECT(Snames = GET_NAMES(x1)); nprotect++;
if (!IS_NUMERIC(x1) || isNull(Snames)) {
UNPROTECT(nprotect);
errorcall(R_NilValue,"in 'init.state': user 'initializer' must return a named numeric vector");
}
nvar = LENGTH(x1);
xp = REAL(x1);
midx = INTEGER(PROTECT(match(Pnames,Snames,0))); nprotect++;
for (j = 0; j < nvar; j++) {
if (midx[j]!=0) {
UNPROTECT(nprotect);
errorcall(R_NilValue,"in 'init.state': a state variable and a parameter share a single name: '%s'",CHARACTER_DATA(STRING_ELT(Snames,j)));
}
}
xdim[0] = nvar; xdim[1] = ns;
PROTECT(x = makearray(2,xdim)); nprotect++;
setrownames(x,Snames,2);
fixdimnames(x,dimnms,2);
xt = REAL(x);
memcpy(xt,xp,nvar*sizeof(double));
for (j = 1, xt += nvar; j < ns; j++, xt += nvar) {
memcpy(pp,p+npar*(j%nrep),npar*sizeof(double));
PROTECT(x2 = eval(fcall,rho));
xp = REAL(x2);
if (LENGTH(x2)!=nvar)
errorcall(R_NilValue,"in 'init.state': user initializer returns vectors of non-uniform length");
memcpy(xt,xp,nvar*sizeof(double));
UNPROTECT(1);
}
}
break;
case native: // use native routine
{
SEXP Cnames;
int *sidx, *pidx, *cidx;
double *xt, *ps, time;
pomp_initializer *ff = NULL;
int j;
PROTECT(Snames = GET_SLOT(pompfun,install("statenames"))); nprotect++;
PROTECT(Cnames = GET_COLNAMES(GET_DIMNAMES(GET_SLOT(object,install("covar"))))); nprotect++;
// construct state, parameter, covariate, observable indices
sidx = INTEGER(PROTECT(name_index(Snames,pompfun,"statenames","state variables"))); nprotect++;
pidx = INTEGER(PROTECT(name_index(Pnames,pompfun,"paramnames","parameters"))); nprotect++;
cidx = INTEGER(PROTECT(name_index(Cnames,pompfun,"covarnames","covariates"))); nprotect++;
// address of native routine
*((void **) (&ff)) = R_ExternalPtrAddr(fn);
nvar = LENGTH(Snames);
xdim[0] = nvar; xdim[1] = ns;
PROTECT(x = makearray(2,xdim)); nprotect++;
setrownames(x,Snames,2);
fixdimnames(x,dimnms,2);
set_pomp_userdata(fcall);
GetRNGstate();
time = *(REAL(t0));
// loop over replicates
for (j = 0, xt = REAL(x), ps = REAL(params); j < ns; j++, xt += nvar)
(*ff)(xt,ps+npar*(j%nrep),time,sidx,pidx,cidx,cp);
PutRNGstate();
unset_pomp_userdata();
}
break;
default:
errorcall(R_NilValue,"in 'init.state': unrecognized 'mode'"); // # nocov
break;
}
}
UNPROTECT(nprotect);
return x;
}
