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#include <map>
#include <string>
#include <sstream>
#include <algorithm>
#include <vector>
#include <stdexcept>
#include <Console.h>
#include <version.h>
#include <util/nainf.h>
#include <R.h>
using std::string;
using std::map;
using std::pair;
using std::vector;
using std::copy;
/* Workaround length being remapped to Rf_length
by the preprocessor */
unsigned long sarray_len(SArray const &s)
{
return s.length();
}
int min2(int a, int b)
{
return std::min(a,b);
}
#include <R.h>
#include <Rinternals.h>
#include <Rdefines.h>
#include <R_ext/Rdynload.h>
std::ostringstream jags_out; //Output stream
std::ostringstream jags_err; //Error stream
static SEXP JAGS_console_tag; //Run-time type checking for external pointer
static bool quiet=false; //Suppress information messages
static void checkConsole (SEXP s)
{
if (TYPEOF(s) != EXTPTRSXP || R_ExternalPtrTag(s) != JAGS_console_tag)
{
error("bad JAGS console pointer");
}
}
static int intArg(SEXP arg)
{
if (!isNumeric(arg)) {
error("Invalid integer parameter");
}
SEXP intarg;
PROTECT(intarg = AS_INTEGER(arg));
int i = INTEGER(intarg)[0];
UNPROTECT(1); //intarg
return i;
}
static char const *stringArg(SEXP arg, unsigned int i = 0)
{
if (!isString(arg)) {
error("Invalid string parameter");
}
return R_CHAR(STRING_ELT(arg,i));
}
static bool boolArg(SEXP arg)
{
if (!isLogical(arg)) {
error("Invalid logical parameter");
}
return LOGICAL_POINTER(arg)[0];
}
static Console * ptrArg(SEXP ptr)
{
checkConsole(ptr);
Console *console = static_cast<Console*>(R_ExternalPtrAddr(ptr));
if (console == NULL)
error("JAGS model must be recompiled");
return console;
}
static void printMessages(bool status)
{
/* Print any messages from JAGS and clear the stream buffer */
if(!jags_out.str().empty()) {
if (!quiet) Rprintf("%s\n", jags_out.str().c_str());
jags_out.str("");
}
string msg;
if (!jags_err.str().empty()) {
msg = jags_err.str();
jags_err.str("");
}
if (status == true) {
if (!msg.empty()) {
warning("%s\n", msg.c_str());
}
}
else {
//Something bad happened
if (!msg.empty()) {
error("%s\n", msg.c_str());
}
else {
error("Internal error in JAGS library");
}
}
}
static void setSArrayValue(SArray &sarray, SEXP e)
{
vector<double> v(length(e));
copy(NUMERIC_POINTER(e), NUMERIC_POINTER(e) + length(e), v.begin());
//Replace R missing values with JAGS missing values
for (vector<double>::iterator p = v.begin(); p != v.end(); ++p) {
if (ISNA(*p)) {
*p = JAGS_NA;
}
}
sarray.setValue(v);
}
/* Write data from an R list into a JAGS data table */
static void writeDataTable(SEXP data, map<string,SArray> &table)
{
SEXP names = getAttrib(data, R_NamesSymbol);
if (!isNewList(data)) {
error("data must be a list");
}
if (length(names) != length(data)) {
error("data must be a named list");
}
for (int i = 0; i < length(data); ++i) {
SEXP e = AS_NUMERIC(VECTOR_ELT(data, i));
if (length(e) > 0) {
string ename = CHAR(STRING_ELT(names, i));
SEXP dim = getAttrib(VECTOR_ELT(data, i), R_DimSymbol);
if (dim == R_NilValue) {
// Scalar or vector entry.
SArray sarray(vector<unsigned int>(1, length(e)));
setSArrayValue(sarray, e);
table.insert(pair<string,SArray>(ename, sarray));
}
else {
// Array entry
int ndim = length(dim);
vector<unsigned int> idim(ndim);
for (int j = 0; j < ndim; ++j) {
idim[j] = INTEGER(dim)[j];
}
SArray sarray(idim);
setSArrayValue(sarray, e);
table.insert(pair<string,SArray>(ename, sarray));
}
}
}
}
static Range makeRange(SEXP lower, SEXP upper)
{
if (lower == R_NilValue || upper == R_NilValue) {
return Range();
}
if (length(lower) != length(upper)) {
error("length mismatch between lower and upper limits");
}
int n = length(lower);
SEXP il, iu;
PROTECT(il = AS_INTEGER(lower));
PROTECT(iu = AS_INTEGER(upper));
vector<int> lvec(n), uvec(n);
copy(INTEGER(il), INTEGER(il) + n, lvec.begin());
copy(INTEGER(iu), INTEGER(iu) + n, uvec.begin());
UNPROTECT(2); //il, iu
Range r;
try {
r = Range(lvec, uvec);
}
catch (std::logic_error except) {
error("Invalid range");
}
return r;
}
/* Read data from a JAGS data table into an R list */
static SEXP readDataTable(map<string,SArray> const &table)
{
int N = table.size();
SEXP data;
PROTECT(data = allocVector(VECSXP, N));
int i;
map<string,SArray>::const_iterator p;
for (i = 0, p = table.begin(); p != table.end(); ++p, ++i) {
int len = sarray_len(p->second);
//Allocate new numeric vector
SEXP e;
PROTECT(e = allocVector(REALSXP, len));
//Copy values
vector<double> const &value = p->second.value();
for (int j = 0; j < len; ++j) {
if (value[j] == JAGS_NA) {
NUMERIC_POINTER(e)[j] = NA_REAL;
}
else {
NUMERIC_POINTER(e)[j] = value[j];
}
}
if (p->second.ndim(false) > 1) {
//Set dim attribute
vector<unsigned int> const &idim = p->second.dim(false);
unsigned int ndim = idim.size();
SEXP dim;
PROTECT(dim = allocVector(INTSXP, ndim));
for (unsigned int k = 0; k < ndim; ++k) {
INTEGER(dim)[k] = idim[k];
}
//Set names of the dimensions
vector<string> const &names = p->second.dimNames();
if (!names.empty()) {
SEXP dimnames;
PROTECT(dimnames = allocVector(STRSXP, ndim));
for (unsigned int k = 0; k < ndim; ++k) {
SET_STRING_ELT(dimnames, k, mkChar(names[k].c_str()));
}
setAttrib(dim, R_NamesSymbol, dimnames);
UNPROTECT(1); //dimnames
}
SET_DIM(e, dim);
UNPROTECT(1); //dim
//Set S dimnames
bool set_s_dimnames = false;
for (unsigned int k = 0; k < ndim; ++k) {
if (!p->second.getSDimNames(k).empty()) {
set_s_dimnames = true;
break;
}
}
if (set_s_dimnames) {
SEXP sdimnames;
PROTECT(sdimnames = allocVector(VECSXP, ndim));
for (unsigned int k = 0; k < ndim; ++k) {
vector<string> const &names_k = p->second.getSDimNames(k);
if (names_k.empty()) {
SET_VECTOR_ELT(sdimnames, k, R_NilValue);
}
else {
SEXP snames_k;
PROTECT(snames_k = allocVector(STRSXP, names_k.size()));
for (unsigned int l = 0; l < names_k.size(); ++l) {
SET_STRING_ELT(sdimnames, l,
mkChar(names_k[l].c_str()));
}
UNPROTECT(1); //snames_k
}
}
setAttrib(e, R_DimNamesSymbol, sdimnames);
UNPROTECT(1); //sdimnames
}
}
else if (!p->second.getSDimNames(0).empty()) {
//Set names attribute
SEXP snames;
vector<string> const &names = p->second.getSDimNames(0);
PROTECT(snames = allocVector(STRSXP, names.size()));
for (unsigned int l = 0; l < names.size(); ++l) {
SET_STRING_ELT(snames, l, mkChar(names[l].c_str()));
}
setAttrib(e, R_NamesSymbol, snames);
UNPROTECT(1); //snames
}
SET_ELEMENT(data, i, e);
UNPROTECT(1); //e
}
//Set names
SEXP names;
PROTECT(names = allocVector(STRSXP, table.size()));
for (i = 0, p = table.begin() ; p != table.end(); ++p, ++i) {
SET_STRING_ELT(names, i, mkChar(p->first.c_str()));
}
setAttrib(data, R_NamesSymbol, names);
UNPROTECT(2); //names, data
return data;
}
static FactoryType asFactoryType(SEXP type)
{
string ft = stringArg(type);
FactoryType ans = SAMPLER_FACTORY;
if (ft == "sampler") {
ans = SAMPLER_FACTORY;
}
else if (ft == "rng") {
ans = RNG_FACTORY;
}
else if (ft == "monitor") {
ans = MONITOR_FACTORY;
}
else {
error("Invalid factory type");
}
return ans;
}
extern "C" {
void quietMessages(SEXP s)
{
quiet = boolArg(s);
}
void R_init_rjags(DllInfo *info)
{
JAGS_console_tag = install("JAGS_CONSOLE_TAG");
}
void R_unload_rjags(DllInfo *info)
{
//FIXME: Need to zero console pointers
vector<string> loaded_modules = Console::listModules();
for (vector<string>::reverse_iterator p = loaded_modules.rbegin();
p != loaded_modules.rend(); ++p)
{
Console::unloadModule(*p);
}
}
SEXP clear_console(SEXP s)
{
/* Finalizer for console pointers. Frees the external memory
and zeroes the pointer when the R object is deleted */
checkConsole(s);
Console *console = static_cast<Console*>(R_ExternalPtrAddr(s));
if (console != NULL) {
delete console;
R_ClearExternalPtr(s);
}
return R_NilValue;
}
SEXP make_console()
{
void *p = static_cast<void*>(new Console(jags_out, jags_err));
SEXP ptr = R_MakeExternalPtr(p, JAGS_console_tag, R_NilValue);
R_RegisterCFinalizer(ptr, (R_CFinalizer_t) clear_console);
return ptr;
}
SEXP check_model(SEXP ptr, SEXP name)
{
/* Name should be a name of a file containing the model */
string sname = R_ExpandFileName(stringArg(name));
FILE *file = fopen(sname.c_str(), "r");
if (!file) {
jags_err << "Failed to open file " << sname << "\n";
return R_NilValue;
}
else {
bool status = ptrArg(ptr)->checkModel(file);
printMessages(status);
fclose(file);
return R_NilValue;
}
}
SEXP compile(SEXP ptr, SEXP data, SEXP nchain, SEXP gendata)
{
if (!isNumeric(nchain)) {
error("nchain must be numeric");
}
if (!isVector(data)) {
error("invalid data");
}
map<string, SArray> table;
writeDataTable(data, table);
bool status = ptrArg(ptr)->compile(table, intArg(nchain),
boolArg(gendata));
printMessages(status);
return R_NilValue;
}
SEXP set_parameters(SEXP ptr, SEXP data, SEXP nchain)
{
map<string,SArray> data_table;
writeDataTable(data, data_table);
bool status = ptrArg(ptr)->setParameters(data_table, intArg(nchain));
printMessages(status);
return R_NilValue;
}
SEXP set_rng_name(SEXP ptr, SEXP name, SEXP chain)
{
bool status = ptrArg(ptr)->setRNGname(stringArg(name), intArg(chain));
printMessages(status);
return R_NilValue;
}
SEXP initialize(SEXP ptr)
{
bool status = ptrArg(ptr)->initialize();
printMessages(status);
return R_NilValue;
}
SEXP check_adaptation(SEXP ptr)
{
Console *console = ptrArg(ptr);
bool status = true;
console->checkAdaptation(status);
return ScalarLogical(status);
}
SEXP is_adapting(SEXP ptr)
{
Console *console = ptrArg(ptr);
return ScalarLogical(console->isAdapting());
}
SEXP adapt_off(SEXP ptr)
{
Console *console = ptrArg(ptr);
console->adaptOff();
return R_NilValue;
}
SEXP update(SEXP ptr, SEXP rniter)
{
int niter = intArg(rniter);
Console *console = ptrArg(ptr);
if (!console->update(niter)) {
Rprintf("\n");
printMessages(false);
}
return R_NilValue;
}
SEXP set_monitors(SEXP ptr, SEXP names, SEXP lower, SEXP upper,
SEXP thin, SEXP type)
{
if (!isString(names)) {
error("names must be a character vector");
}
int n = length(names);
if (length(lower) != n || length(upper) != n) {
error("length of names must match length of lower and upper");
}
SEXP status; //Was attempt to set monitor successful?
PROTECT(status = allocVector(LGLSXP, n));
for (int i = 0; i < n; ++i) {
Range range = makeRange(VECTOR_ELT(lower, i), VECTOR_ELT(upper, i));
bool ok = ptrArg(ptr)->setMonitor(stringArg(names,i), range,
intArg(thin),
stringArg(type));
printMessages(true);
LOGICAL_POINTER(status)[i] = ok;
}
UNPROTECT(1); //status
return status;
}
SEXP clear_monitor(SEXP ptr, SEXP name, SEXP lower, SEXP upper, SEXP type)
{
Range range = makeRange(lower, upper);
bool status = ptrArg(ptr)->clearMonitor(stringArg(name), range,
stringArg(type));
printMessages(status);
return R_NilValue;
}
SEXP get_monitored_values(SEXP ptr, SEXP type)
{
map<string,SArray> data_table;
bool status = ptrArg(ptr)->dumpMonitors(data_table, stringArg(type),
false);
printMessages(status);
return readDataTable(data_table);
}
//FIXME: lazy cut-and-paste here
SEXP get_monitored_values_flat(SEXP ptr, SEXP type)
{
map<string,SArray> data_table;
bool status = ptrArg(ptr)->dumpMonitors(data_table, stringArg(type),
true);
printMessages(status);
return readDataTable(data_table);
}
SEXP get_data(SEXP ptr)
{
map<string,SArray> data_table;
string rngname; //Not actually needed
bool status = ptrArg(ptr)->dumpState(data_table, rngname, DUMP_DATA, 1);
printMessages(status);
return readDataTable(data_table);
}
SEXP get_state(SEXP ptr)
{
Console *console = ptrArg(ptr);
unsigned int nchain = console->nchain();
if (nchain == 0) {
return R_NilValue;
}
//ans is the list that contains the state for each chain
SEXP ans;
PROTECT(ans = allocVector(VECSXP, nchain));
for (unsigned int n = 0; n < nchain; ++n) {
string srng;
map<string,SArray> param_table;
console->dumpState(param_table, srng, DUMP_PARAMETERS, n+1);
//Read the parameter values into an R list
SEXP params;
PROTECT(params = readDataTable(param_table));
int nparam = length(params);
SEXP names = getAttrib(params, R_NamesSymbol);
//Now we have to make a copy of the list with an extra element
SEXP staten, namesn;
PROTECT(staten = allocVector(VECSXP, nparam + 1));
PROTECT(namesn = allocVector(STRSXP, nparam + 1));
for (int j = 0; j < nparam; ++j) {
SET_ELEMENT(staten, j, VECTOR_ELT(params, j));
SET_STRING_ELT(namesn, j, STRING_ELT(names, j));
}
//Assign .RNG.name as the last element
SEXP rngname;
PROTECT(rngname = mkString(srng.c_str()));
SET_ELEMENT(staten, nparam, rngname);
SET_STRING_ELT(namesn, nparam, mkChar(".RNG.name"));
setAttrib(staten, R_NamesSymbol, namesn);
//And we're done with this chain
SET_ELEMENT(ans, n, staten);
UNPROTECT(4); //rngname, namesn, staten, params
}
UNPROTECT(1); //ans
return ans;
}
SEXP get_variable_names(SEXP ptr)
{
Console *console = ptrArg(ptr);
vector<string> const &namevec = console->variableNames();
SEXP varnames;
PROTECT(varnames = allocVector(STRSXP,namevec.size()));
for (unsigned int i = 0; i < namevec.size(); ++i) {
SET_STRING_ELT(varnames, i, mkChar(namevec[i].c_str()));
}
UNPROTECT(1); //varnames
return varnames;
}
SEXP get_samplers(SEXP ptr)
{
Console *console = ptrArg(ptr);
vector<vector<string> > samplers;
bool status = console->dumpSamplers(samplers);
printMessages(status);
unsigned int n = samplers.size();
SEXP node_list, sampler_names;
PROTECT(node_list = allocVector(VECSXP, n));
PROTECT(sampler_names = allocVector(STRSXP, n));
for (unsigned int i = 0; i < n; ++i) {
int nnode = samplers[i].size() - 1;
SEXP e;
PROTECT(e=allocVector(STRSXP, nnode));
for (int j = 0; j < nnode; ++j) {
SET_STRING_ELT(e, j, mkChar(samplers[i][j+1].c_str()));
}
SET_ELEMENT(node_list, i, e);
SET_STRING_ELT(sampler_names, i, mkChar(samplers[i][0].c_str()));
UNPROTECT(1); //e
}
setAttrib(node_list, R_NamesSymbol, sampler_names);
UNPROTECT(2); //node_list, sampler_names
return node_list;
}
SEXP get_factories(SEXP type)
{
FactoryType ft = asFactoryType(type);
vector<pair<string, bool> > factories = Console::listFactories(ft);
unsigned int n = factories.size();
SEXP fac_list;
PROTECT(fac_list = allocVector(VECSXP, 2));
SEXP names, status;
PROTECT(names = allocVector(STRSXP, n));
PROTECT(status = allocVector(LGLSXP, n));
for (unsigned int i = 0; i < n; ++i) {
SET_STRING_ELT(names, i, mkChar(factories[i].first.c_str()));
LOGICAL_POINTER(status)[i] = factories[i].second;
}
SET_ELEMENT(fac_list, 0, names);
SET_ELEMENT(fac_list, 1, status);
UNPROTECT(2); //names, status
SEXP fac_names;
PROTECT(fac_names = allocVector(STRSXP,2));
SET_STRING_ELT(fac_names, 0, mkChar("factory"));
SET_STRING_ELT(fac_names, 1, mkChar("status"));
setAttrib(fac_list, R_NamesSymbol, fac_names);
UNPROTECT(1); //fac_names
UNPROTECT(1); //fac_list
return fac_list;
}
SEXP set_factory_active(SEXP name, SEXP type, SEXP status)
{
Console::setFactoryActive(stringArg(name), asFactoryType(type),
boolArg(status));
return R_NilValue;
}
SEXP get_iter(SEXP ptr)
{
return ScalarInteger(ptrArg(ptr)->iter());
}
SEXP get_nchain(SEXP ptr)
{
return ScalarInteger(ptrArg(ptr)->nchain());
}
SEXP load_module(SEXP name)
{
return ScalarLogical(Console::loadModule(stringArg(name)));
}
SEXP unload_module(SEXP name)
{
return ScalarLogical(Console::unloadModule(stringArg(name)));
}
SEXP get_modules()
{
vector<string> modules = Console::listModules();
unsigned int n = modules.size();
SEXP mod_list;
PROTECT(mod_list = allocVector(STRSXP, n));
for (unsigned int i = 0; i < n; ++i) {
SET_STRING_ELT(mod_list, i, mkChar(modules[i].c_str()));
}
UNPROTECT(1); //mod_list
return mod_list;
}
SEXP get_version()
{
return mkString(jags_version());
}
}