src: use d instead of p for dimension

Author: Carol-seven

src/ADMM.cpp

@@ -13,14 +13,14 @@ List ADMMsggl(const arma::mat& S, const List& group_idx,
               double rho, const double tau_incr, const double tau_decr, const double nu,
               const double tol_abs, const double tol_rel, const int maxiter) {
 
-  int p = S.n_cols;
+  int d = S.n_cols;
   int iter = 0;
   arma::mat Omega = arma::diagmat(1/arma::diagvec(S));
-  arma::mat Z = arma::zeros(p, p);
-  arma::mat U = arma::zeros(p, p);
+  arma::mat Z = arma::zeros(d, d);
+  arma::mat U = arma::zeros(d, d);
   arma::mat Z_old = Z;
 
-  arma::mat I = arma::ones(p, p);
+  arma::mat I = arma::ones(d, d);
   if (!diag_ind) {
     I -= arma::diagmat(I);
   }
@@ -65,13 +65,13 @@ List ADMMsggl(const arma::mat& S, const List& group_idx,
           Z_block *= scale_grp;
         } else {
           double sq_all = arma::accu(arma::square(Z_block));
-          arma::vec d = Z_diag.elem(row_idx);
-          double sq_diag = arma::dot(d, d);
+          arma::vec de = Z_diag.elem(row_idx);
+          double sq_diag = arma::dot(de, de);
           double offblock_norm = std::sqrt(std::max(sq_all-sq_diag, 0.0));
           double scale_grp = std::max(1.0 - lambda * (1-alpha) / (rho * (offblock_norm + eps)), 0.0);
           Z_block *= scale_grp;
           for (arma::uword k = 0; k < row_idx.n_elem; ++k) {
-            Z(row_idx[k], row_idx[k]) = d[k];
+            Z(row_idx[k], row_idx[k]) = de[k];
           }
         }
       }
@@ -85,8 +85,8 @@ List ADMMsggl(const arma::mat& S, const List& group_idx,
     double s = arma::norm(rho*(Z - Z_old), "fro");
 
     // tolerance
-    double tol_pri = p * tol_abs + tol_rel * std::max(arma::norm(Omega, "fro"), arma::norm(Z, "fro"));
-    double tol_dual = p * tol_abs + tol_rel * rho * arma::norm(U, "fro");
+    double tol_pri = d * tol_abs + tol_rel * std::max(arma::norm(Omega, "fro"), arma::norm(Z, "fro"));
+    double tol_dual = d * tol_abs + tol_rel * rho * arma::norm(U, "fro");
 
     if (r <= tol_pri && s <= tol_dual) {
       break;
@@ -124,18 +124,18 @@ List ADMMsggn(const arma::mat& S, const List& group_idx, std::string penalty,
               double rho, const double tau_incr, const double tau_decr, const double nu,
               const double tol_abs, const double tol_rel, const int maxiter) {
 
-  int p = S.n_cols;
+  int d = S.n_cols;
   int iter = 0;
   arma::mat Omega = arma::diagmat(1/arma::diagvec(S));
-  arma::mat Z = arma::zeros(p, p);
-  arma::mat U = arma::zeros(p, p);
+  arma::mat Z = arma::zeros(d, d);
+  arma::mat U = arma::zeros(d, d);
   arma::mat Z_old = Z;
   List sgglres = ADMMsggl(S, group_idx, diag_ind, diag_grp, diag_include, lambda, alpha,
                           rho, tau_incr, tau_decr, nu,
                           tol_abs, tol_rel, maxiter);
   arma::mat initial = sgglres["hatOmega"];
 
-  arma::mat I = arma::ones(p, p);
+  arma::mat I = arma::ones(d, d);
   if (!diag_ind) {
     I -= arma::diagmat(I);
   }
@@ -164,8 +164,8 @@ List ADMMsggn(const arma::mat& S, const List& group_idx, std::string penalty,
     double s = arma::norm(rho*(Z - Z_old), "fro");
 
     // tolerance
-    double tol_pri = p * tol_abs + tol_rel * std::max(arma::norm(Omega, "fro"), arma::norm(Z, "fro"));
-    double tol_dual = p * tol_abs + tol_rel * rho * arma::norm(U, "fro");
+    double tol_pri = d * tol_abs + tol_rel * std::max(arma::norm(Omega, "fro"), arma::norm(Z, "fro"));
+    double tol_dual = d * tol_abs + tol_rel * rho * arma::norm(U, "fro");
 
     if (r <= tol_pri && s <= tol_dual) {
       break;

src/update_.cpp

@@ -55,13 +55,13 @@ arma::mat update_Zblock(const arma::mat& M, const std::string& penalty,
         Z_block *= scale_grp;
       } else {
         double sq_all = arma::accu(arma::square(Z_block));
-        arma::vec d = Z_diag.elem(row_idx);
-        double sq_diag = arma::dot(d, d);
+        arma::vec de = Z_diag.elem(row_idx);
+        double sq_diag = arma::dot(de, de);
         double offblock_norm = std::sqrt(std::max(sq_all-sq_diag, 0.0));
         double scale_grp = std::max(1.0 - lambda_grp * (1-alpha) / (rho * (offblock_norm + eps)), 0.0);
         Z_block *= scale_grp;
         for (arma::uword k = 0; k < row_idx.n_elem; ++k) {
-          Z(row_idx[k], row_idx[k]) = d[k];
+          Z(row_idx[k], row_idx[k]) = de[k];
         }
       }
     }

src/utils.cpp

@@ -26,7 +26,7 @@ double criterion(const arma::mat& hatOmega, const arma::mat& S, int n,
                  const std::string& crit, double ebic_tuning) {
 
   // dimensionality
-  int p = S.n_cols;
+  int d = S.n_cols;
   // Gaussian log-likelihood
   double sign, logdet;
   arma::log_det(logdet, sign, hatOmega);
@@ -49,10 +49,10 @@ double criterion(const arma::mat& hatOmega, const arma::mat& S, int n,
     return -2*loglik + std::log(n)*edges;
   }
   else if (crit == "EBIC") {
-    return -2*loglik + std::log(n)*edges + 4*ebic_tuning*std::log(p)*edges;
+    return -2*loglik + std::log(n)*edges + 4*ebic_tuning*std::log(d)*edges;
   }
   else if (crit == "HBIC") {
-    return -2*loglik + std::log(std::log(n))*std::log(p)*edges;
+    return -2*loglik + std::log(std::log(n))*std::log(d)*edges;
   }
   else {
     Rcpp::stop("Unknown criterion!");