Removed graph until fixed, keep main stable

KellisLab · Feb 8, 2024 · 94966c3 · 94966c3
1 parent 4ebae50
commit 94966c3
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diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,26 +1,6 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-r_bigclam_init <- function(X, n_comm) {
-    .Call('_scdemon_r_bigclam_init', PACKAGE = 'scdemon', X, n_comm)
-}
-
-r_bigclam <- function(C, n_comm, max_iter = 1000L) {
-    .Call('_scdemon_r_bigclam', PACKAGE = 'scdemon', C, n_comm, max_iter)
-}
-
-r_graph_conductance <- function(X, min_deg) {
-    .Call('_scdemon_r_graph_conductance', PACKAGE = 'scdemon', X, min_deg)
-}
-
-r_graph_conductance_row <- function(X, i, degree, deg_sum, min_deg) {
-    .Call('_scdemon_r_graph_conductance_row', PACKAGE = 'scdemon', X, i, degree, deg_sum, min_deg)
-}
-
-r_graph_degree <- function(X, diag = FALSE) {
-    .Call('_scdemon_r_graph_degree', PACKAGE = 'scdemon', X, diag)
-}
-
 r_ols_beta <- function(X, Y) {
     .Call('_scdemon_r_ols_beta', PACKAGE = 'scdemon', X, Y)
 }

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -11,70 +11,6 @@ Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
 Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
-// r_bigclam_init
-Eigen::MatrixXd r_bigclam_init(const Eigen::Map<Eigen::SparseMatrix<double> >& X, int n_comm);
-RcppExport SEXP _scdemon_r_bigclam_init(SEXP XSEXP, SEXP n_commSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::Map<Eigen::SparseMatrix<double> >& >::type X(XSEXP);
-    Rcpp::traits::input_parameter< int >::type n_comm(n_commSEXP);
-    rcpp_result_gen = Rcpp::wrap(r_bigclam_init(X, n_comm));
-    return rcpp_result_gen;
-END_RCPP
-}
-// r_bigclam
-Eigen::ArrayXXd r_bigclam(const Eigen::Map<Eigen::SparseMatrix<double> >& C, int n_comm, int max_iter);
-RcppExport SEXP _scdemon_r_bigclam(SEXP CSEXP, SEXP n_commSEXP, SEXP max_iterSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::Map<Eigen::SparseMatrix<double> >& >::type C(CSEXP);
-    Rcpp::traits::input_parameter< int >::type n_comm(n_commSEXP);
-    Rcpp::traits::input_parameter< int >::type max_iter(max_iterSEXP);
-    rcpp_result_gen = Rcpp::wrap(r_bigclam(C, n_comm, max_iter));
-    return rcpp_result_gen;
-END_RCPP
-}
-// r_graph_conductance
-Eigen::ArrayXd r_graph_conductance(const Eigen::Map<Eigen::SparseMatrix<double> >& X, int min_deg);
-RcppExport SEXP _scdemon_r_graph_conductance(SEXP XSEXP, SEXP min_degSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::Map<Eigen::SparseMatrix<double> >& >::type X(XSEXP);
-    Rcpp::traits::input_parameter< int >::type min_deg(min_degSEXP);
-    rcpp_result_gen = Rcpp::wrap(r_graph_conductance(X, min_deg));
-    return rcpp_result_gen;
-END_RCPP
-}
-// r_graph_conductance_row
-double r_graph_conductance_row(const Eigen::Map<Eigen::SparseMatrix<double> >& X, Eigen::Index i, const Eigen::ArrayXd& degree, double deg_sum, int min_deg);
-RcppExport SEXP _scdemon_r_graph_conductance_row(SEXP XSEXP, SEXP iSEXP, SEXP degreeSEXP, SEXP deg_sumSEXP, SEXP min_degSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::Map<Eigen::SparseMatrix<double> >& >::type X(XSEXP);
-    Rcpp::traits::input_parameter< Eigen::Index >::type i(iSEXP);
-    Rcpp::traits::input_parameter< const Eigen::ArrayXd& >::type degree(degreeSEXP);
-    Rcpp::traits::input_parameter< double >::type deg_sum(deg_sumSEXP);
-    Rcpp::traits::input_parameter< int >::type min_deg(min_degSEXP);
-    rcpp_result_gen = Rcpp::wrap(r_graph_conductance_row(X, i, degree, deg_sum, min_deg));
-    return rcpp_result_gen;
-END_RCPP
-}
-// r_graph_degree
-Eigen::ArrayXd r_graph_degree(const Eigen::Map<Eigen::SparseMatrix<double> >& X, bool diag);
-RcppExport SEXP _scdemon_r_graph_degree(SEXP XSEXP, SEXP diagSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::Map<Eigen::SparseMatrix<double> >& >::type X(XSEXP);
-    Rcpp::traits::input_parameter< bool >::type diag(diagSEXP);
-    rcpp_result_gen = Rcpp::wrap(r_graph_degree(X, diag));
-    return rcpp_result_gen;
-END_RCPP
-}
 // r_ols_beta
 Eigen::MatrixXd r_ols_beta(const Eigen::Map<Eigen::MatrixXd>& X, const Eigen::Map<Eigen::MatrixXd>& Y);
 RcppExport SEXP _scdemon_r_ols_beta(SEXP XSEXP, SEXP YSEXP) {
@@ -128,11 +64,6 @@ END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_scdemon_r_bigclam_init", (DL_FUNC) &_scdemon_r_bigclam_init, 2},
-    {"_scdemon_r_bigclam", (DL_FUNC) &_scdemon_r_bigclam, 3},
-    {"_scdemon_r_graph_conductance", (DL_FUNC) &_scdemon_r_graph_conductance, 2},
-    {"_scdemon_r_graph_conductance_row", (DL_FUNC) &_scdemon_r_graph_conductance_row, 5},
-    {"_scdemon_r_graph_degree", (DL_FUNC) &_scdemon_r_graph_degree, 2},
     {"_scdemon_r_ols_beta", (DL_FUNC) &_scdemon_r_ols_beta, 2},
     {"_scdemon_r_ols_resid", (DL_FUNC) &_scdemon_r_ols_resid, 3},
     {"_scdemon_r_robust_se_X", (DL_FUNC) &_scdemon_r_robust_se_X, 2},

diff --git a/src/bigclam.hpp b/src/bigclam.hpp
diff --git a/src/graph.hpp b/src/graph.hpp
diff --git a/src/r_bigclam.cpp b/src/r_bigclam.cpp
diff --git a/src/r_graph.cpp b/src/r_graph.cpp