void graphConvert(SEXP graph_sexp, residualConnectivity::context::inputGraph& boostGraph, std::vector<residualConnectivity::context::vertexPosition>& vertexCoordinates)
{
Rcpp::RObject graph = Rcpp::as<Rcpp::RObject>(graph_sexp);
std::string className = Rcpp::as<std::string>(graph.attr("class"));
Rcpp::NumericMatrix vertexCoordinates_matrix;
if(className == "igraph")
{
Rcpp::Environment igraphEnv("package:igraph");
Rcpp::Function isDirected = igraphEnv["is_directed"];
if(Rcpp::as<bool>(isDirected(graph)))
{
throw std::runtime_error("Input `graph' must be undirected");
}
Rcpp::Function layoutAuto = igraphEnv["layout.auto"];
vertexCoordinates_matrix = layoutAuto(graph);
igraphConvert(graph_sexp, boostGraph);
}
else if(className == "graphNEL" || className == "graphAM")
{
Rcpp::S4 graphS4 = Rcpp::as<Rcpp::S4>(graph);
Rcpp::S4 renderInfo = Rcpp::as<Rcpp::S4>(graphS4.slot("renderInfo"));
Rcpp::List nodes = Rcpp::as<Rcpp::List>(renderInfo.slot("nodes"));
Rcpp::Function length("length"), cbind("cbind");
if(Rcpp::as<int>(length(nodes)) > 0)
{
vertexCoordinates_matrix = Rcpp::as<Rcpp::NumericMatrix>(cbind(nodes["nodeX"], nodes["nodeY"]));
}
if(className == "graphNEL") graphNELConvert(graph_sexp, boostGraph);
else graphAMConvert(graph_sexp, boostGraph);
}
else
{
throw std::runtime_error("Input graph must have class \"igraph\", \"graphAM\" or \"graphNEL\"");
}
std::size_t nVertexCoordinates = vertexCoordinates_matrix.nrow();
vertexCoordinates.clear();
vertexCoordinates.reserve(nVertexCoordinates);
for(std::size_t i = 0; i < nVertexCoordinates; i++)
{
vertexCoordinates.push_back(residualConnectivity::context::vertexPosition((residualConnectivity::context::vertexPosition::first_type)vertexCoordinates_matrix((int)i, 0), (residualConnectivity::context::vertexPosition::second_type)vertexCoordinates_matrix((int)i, 1)));
}
}
DenseMatrix buildDenseMatrix(const std::string& expr1,
const std::string& expr2,
const MatrixReaderOptions& options)
{
auto m1 = readDenseMatrix(expr1, options);
if(expr2 != "") {
auto m2 = readDenseMatrix(expr2, options);
m1.cbind(m2);
}
return m1;
}
MVTR::MvtRegModel(const Mat &X,const Mat &Y, bool add_intercept)
: ParamPolicy(new MatrixParams(X.ncol() + add_intercept,Y.ncol()),
new SpdParams(Y.ncol()),
new UnivParams(default_df))
{
Mat XX(add_intercept? cbind(1.0,X) : X);
QR qr(XX);
Mat Beta(qr.solve(qr.QtY(Y)));
Mat resid = Y - XX* Beta;
uint n = XX.nrow();
Spd Sig = resid.t() * resid/n;
set_Beta(Beta);
set_Sigma(Sig);
for(uint i=0; i<n; ++i){
Vec y = Y.row(i);
Vec x = XX.row(i);
NEW(MvRegData, dp)(y,x);
DataPolicy::add_data(dp);
}
}
Matrix add_intercept(const Matrix &X){
Vector one(X.nrow(), 1.0);
return cbind(one, X); }
