void IGMeasurementError::initFromList(Rcpp::List const &init_list)
{
NormalVarianceMixtureBaseError::initFromList(init_list);
if(init_list.containsElementNamed("nu"))
nu = Rcpp::as < double >( init_list["nu"]);
else
nu = 1.;
EV = 1.; // not true it is the mode is alpha/(alpha - 1)
EiV = 1.;
npars += 1;
digamma_nu = Digamma(nu);
trigamma_nu = Trigamma(nu);
int i = 0;
if( init_list.containsElementNamed("Vs" )){
Rcpp::List Vs_list = init_list["Vs"];
Vs.resize(Vs_list.length());
for( Rcpp::List::iterator it = Vs_list.begin(); it != Vs_list.end(); ++it ) {
Vs[i++] = Rcpp::as < Eigen::VectorXd >( it[0]);
}
}else
throw("in IGMeasurementError::initFromList Vs must be set! \n");
}
void NormalVarianceMixtureBaseError::initFromList(Rcpp::List const &init_list)
{
if(init_list.containsElementNamed("sigma"))
sigma = Rcpp::as < double >( init_list["sigma"]);
else
sigma = 1.;
npars += 1;
if(init_list.containsElementNamed("common_V"))
common_V = Rcpp::as < int >( init_list["common_V"]);
else
common_V = 0;
int i = 0;
if( init_list.containsElementNamed("Vs" )){
Rcpp::List Vs_list = init_list["Vs"];
Vs.resize(Vs_list.length());
for( Rcpp::List::iterator it = Vs_list.begin(); it != Vs_list.end(); ++it ) {
Vs[i++] = Rcpp::as < Eigen::VectorXd >( it[0]);
}
}else
throw("in NormalVarianceMixtureBaseError::initFromList Vs must be set! \n");
}
void RSim::setInputSpikes(const Rcpp::List &l, const string &obj_name) {
Ptr<SerializableBase> sp_l;
if(l.containsElementNamed("values")) {
sp_l = RProto::convertFromR<SerializableBase>(l);
} else {
try {
Rcpp::List sl;
sl["values"] = l;
sl.attr("class") = "SpikesList";
sp_l = RProto::convertFromR<SerializableBase>(sl);
} catch (...) {
ERR("Expecting list with spike times of neurons or SpikesList list object\n");
}
}
auto slice = Factory::inst().getObjectsSlice(obj_name);
for(auto it=slice.first; it != slice.second; ++it) {
Factory::inst().getObject(it)->setAsInput(
sp_l
);
}
net->spikesList().info = sp_l.as<SpikesList>()->info;
for(auto &n: neurons) {
n.ref().initInternal();
}
}
void constMatrix::initFromList(Rcpp::List const & init_list)
{
npars = 1;
std::vector<std::string> check_names = {"Q","loc", "h"};
check_Rcpplist(init_list, check_names, "constMatrix::initFromList");
Q = Rcpp::as<Eigen::SparseMatrix<double,0,int> >(init_list["Q"]);
d = Q.rows();
int nIter = Rcpp::as<double>(init_list["nIter"]);
tauVec.resize(nIter+1);
npars = 0;
v.setZero(1);
m.resize(1,1);
tau = 1.;
if(init_list.containsElementNamed("tau"))
tau = Rcpp::as<double >( init_list["tau"]);
Q *= tau;
dtau = 0.;
ddtau = 0.;
counter = 0;
tauVec[counter] = tau;
counter++;
loc = Rcpp::as< Eigen::VectorXd >(init_list["loc"]);
h = Rcpp::as< Eigen::VectorXd >(init_list["h"]);
h_average = h.sum() / h.size();
m_loc = loc.minCoeff();
}
SEXP stochasticEnumeration(SEXP nVertices_sexp, SEXP budget_sexp, SEXP seed_sexp, SEXP options_sexp)
{
BEGIN_RCPP
int seed = Rcpp::as<int>(seed_sexp);
int nVertices = Rcpp::as<int>(nVertices_sexp);
int budget = Rcpp::as<int>(budget_sexp);
Rcpp::List options = options_sexp;
bool outputSamples = false;
if(!options.containsElementNamed("reduceChains")) throw std::runtime_error("Unable to find option named reduceChains");
if(!options.containsElementNamed("graphRepresentation")) throw std::runtime_error("Unable to find option named graphRepresentation");
bool reduceChains = Rcpp::as<bool>(options("reduceChains"));
std::string graphRepresentationString = Rcpp::as<std::string>(options("graphRepresentation"));
graphRepresentation representation = toRepresentation(graphRepresentationString);
if (options.containsElementNamed("outputSamples"))
{
outputSamples = Rcpp::as<bool>(options("outputSamples"));
}
boost::mt19937 randomSource;
randomSource.seed(seed);
chordalGraph::stochasticEnumerationArgs args(randomSource);
args.nVertices = nVertices;
args.budget = budget;
args.outputSamples = outputSamples;
int maxEdges = ((nVertices - 1)*nVertices / 2);
//Set up text progress bar
Rcpp::Function txtProgressBar("txtProgressBar");
Rcpp::Function close("close");
Rcpp::Function setTxtProgressBar("setTxtProgressBar");
Rcpp::RObject barHandle = txtProgressBar(Rcpp::Named("style") = 3, Rcpp::Named("min") = 0, Rcpp::Named("max") = maxEdges, Rcpp::Named("initial") = 0);
//List for samples
Rcpp::List samples(maxEdges+1);
std::vector<bool> exactVector;
std::vector<int> minimumSizeForExactVector;
std::vector<std::string> estimatesAsStrings;
for (int nEdges = 0; nEdges < maxEdges+1; nEdges++)
{
setTxtProgressBar(barHandle, nEdges);
args.nEdges = nEdges;
args.samples.clear();
if(reduceChains)
{
if(representation == listRepresentation)
{
chordalGraph::stochasticEnumerationReduceChains<chordalGraph::cliqueTree>(args);
}
else
{
chordalGraph::stochasticEnumerationReduceChains<chordalGraph::cliqueTreeAdjacencyMatrix>(args);
}
}
else
{
if(representation == listRepresentation)
{
chordalGraph::stochasticEnumeration<chordalGraph::cliqueTree>(args);
}
else
{
chordalGraph::stochasticEnumeration<chordalGraph::cliqueTreeAdjacencyMatrix>(args);
}
}
estimatesAsStrings.push_back(args.estimate.str());
exactVector.push_back(args.exact);
if (args.outputSamples)
{
Rcpp::List currentEdgesSamples;
convert(currentEdgesSamples, args.samples);
samples[nEdges] = currentEdgesSamples;
}
if(args.minimumSizeForExact == -1)
{
minimumSizeForExactVector.push_back(NA_INTEGER);
}
else
{
minimumSizeForExactVector.push_back(args.minimumSizeForExact);
}
}
close(barHandle);
SEXP estimatesAsStrings_sexp = Rcpp::wrap(estimatesAsStrings);
SEXP minimumSizeForExactVector_sexp = Rcpp::wrap(minimumSizeForExactVector);
Rcpp::Function mpfrFunction("mpfr");
Rcpp::List listResult = Rcpp::List::create(Rcpp::Named("data") = mpfrFunction(estimatesAsStrings_sexp, Rcpp::Named("prec", 50)), Rcpp::Named("exact") = Rcpp::wrap(exactVector), Rcpp::Named("minimumSizeForExact") = minimumSizeForExactVector_sexp);
if (args.outputSamples)
{
listResult("samples") = samples;
}
return listResult;
END_RCPP
}
SEXP stochasticEnumerationSpecificEdges(SEXP nVertices_sexp, SEXP nEdges_sexp, SEXP budget_sexp, SEXP seed_sexp, SEXP options_sexp)
{
BEGIN_RCPP
int seed = Rcpp::as<int>(seed_sexp);
int nVertices = Rcpp::as<int>(nVertices_sexp);
int nEdges = Rcpp::as<int>(nEdges_sexp);
int budget = Rcpp::as<int>(budget_sexp);
Rcpp::List options = options_sexp;
bool outputSamples = false;
if(!options.containsElementNamed("reduceChains")) throw std::runtime_error("Unable to find option named reduceChains");
if(!options.containsElementNamed("graphRepresentation")) throw std::runtime_error("Unable to find option named graphRepresentation");
bool reduceChains = Rcpp::as<bool>(options("reduceChains"));
std::string graphRepresentationString = Rcpp::as<std::string>(options("graphRepresentation"));
graphRepresentation representation = toRepresentation(graphRepresentationString);
if (options.containsElementNamed("outputSamples"))
{
outputSamples = Rcpp::as<bool>(options("outputSamples"));
}
boost::mt19937 randomSource;
randomSource.seed(seed);
chordalGraph::stochasticEnumerationArgs args(randomSource);
args.nEdges = nEdges;
args.nVertices = nVertices;
args.budget = budget;
args.outputSamples = outputSamples;
if(reduceChains)
{
if(representation == listRepresentation)
{
chordalGraph::stochasticEnumerationReduceChains<chordalGraph::cliqueTree>(args);
}
else
{
chordalGraph::stochasticEnumerationReduceChains<chordalGraph::cliqueTreeAdjacencyMatrix>(args);
}
}
else
{
if(representation == listRepresentation)
{
chordalGraph::stochasticEnumeration<chordalGraph::cliqueTree>(args);
}
else
{
chordalGraph::stochasticEnumeration<chordalGraph::cliqueTreeAdjacencyMatrix>(args);
}
}
std::string estimateAsString = args.estimate.str();
SEXP estimateAsString_sexp = Rcpp::wrap(estimateAsString);
SEXP minimumSizeForExact_sexp;
if(args.minimumSizeForExact != -1) minimumSizeForExact_sexp = Rcpp::wrap(args.minimumSizeForExact);
else minimumSizeForExact_sexp = Rcpp::wrap(NA_INTEGER);
Rcpp::Function mpfrFunction("mpfr");
Rcpp::List listResult = Rcpp::List::create(Rcpp::Named("data") = mpfrFunction(estimateAsString_sexp, Rcpp::Named("prec", 50)), Rcpp::Named("exact") = Rcpp::wrap(args.exact), Rcpp::Named("minimumSizeForExact") = minimumSizeForExact_sexp);
if (args.outputSamples)
{
Rcpp::List samples;
convert(samples, args.samples);
listResult("samples") = samples;
}
return listResult;
END_RCPP
}