update QRWMR

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.0
-Date: 2022-08-17 21:15:59 UTC
-SHA: 9e26b77dc5aeb764214c63eb665d892685bba329
+Version: 1.0.1
+Date: 2024-02-22 02:19:13 UTC
+SHA: 82b6d6aecea6a19861c56747df859ca61158c0bf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: regnet
 Type: Package
 Title: Network-Based Regularization for Generalized Linear Models
-Version: 1.0.1
+Version: 1.0.2
 Author: Jie Ren, Luann C. Jung, Yinhao Du, Cen Wu, Yu Jiang, Junhao Liu
 Maintainer: Jie Ren <[email protected]>
 Description: Network-based regularization has achieved success in variable selection for 
@@ -18,7 +18,7 @@ LazyData: true
 Imports: glmnet, stats, Rcpp, igraph, utils
 URL: https://github.com/jrhub/regnet
 BugReports: https://github.com/jrhub/regnet/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LinkingTo: Rcpp, RcppArmadillo
 Suggests: 
     testthat,

R/plot.regnet.R

@@ -16,7 +16,6 @@
 #' @return an object of class "igraph" is returned in default.
 #' When \emph{subnetworks=TRUE}, a list of "igraph" objects (sub-networks) is returned.
 #'
-#' @usage \method{plot}{regnet}(x, subnetworks=FALSE, vsize=10, labelDist=2, minVertices=2, theta=5, \dots)
 #' @seealso \code{\link{regnet}}
 #'
 #' @examples
@@ -36,14 +35,15 @@ plot.regnet=function(x, subnetworks=FALSE, vsize=10, labelDist=2, minVertices=2,
 
   adjacency = x$Adj
   if(nrow(adjacency)==0) return(NULL)
-  net0 <- igraph::graph.adjacency(adjacency, mode="undirected", weighted=TRUE, diag=FALSE)
+  # net0 <- igraph::graph.adjacency(adjacency, mode="undirected", weighted=TRUE, diag=FALSE)
+  net0 <- igraph::graph_from_adjacency_matrix(adjacency, mode="undirected", weighted=TRUE, diag=FALSE)
   igraph::V(net0)$color = "skyblue"
 
   if(!subnetworks){
     plot(net0, vertex.size=vsize, edge.color="gray40", vertex.label=NA)
     net0
   }else{
-    nets = igraph::decompose.graph(net0, mode="weak", min.vertices = minVertices)
+    nets = igraph::decompose(net0, mode="weak", min.vertices = minVertices)
     largest = 0
     if(length(nets)==0) return(NULL)
     for(i in 1: length(nets)){

README.md

@@ -38,7 +38,7 @@ available for continuous and survival responses.
 <!-- -->
 
     install.packages("devtools")
-    devtools::install_github("jrhub/regnet")
+    devtools::install_github("jrhub/regnet") #v1.0.2
 
 - Released versions of regnet are available on CRAN
   [(link)](https://cran.r-project.org/package=regnet), and can be

regnet.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 641f086e-8023-4b4b-b547-3b0a0d51ef10
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

src/QR.cpp

@@ -6,18 +6,25 @@ using namespace Rcpp;
 using namespace arma;
 
 
-arma::vec QRWMR(arma::mat const &x, arma::vec const &y, arma::vec b)
+arma::vec QRWMR(arma::mat const &x, arma::vec const &y, arma::vec b, bool debugging)
 {
   int p = x.n_cols, n = x.n_rows;
   arma::vec t = y - x * b;
   arma::vec u(n, fill::none), w(n, fill::none);
   arma::uvec index;
-  
+
   for(int m = 0; m < p; m++){
     t += x.col(m) * b(m);
     u = t/x.col(m);
     w = arma::abs(x.col(m))/n;
-
+
+    u.replace(datum::nan, 0);
+
+    if (debugging) {
+      Rcpp::Rcout << "Values of u before NaN replacement for column " << m << ":\n";
+      u.print(Rcpp::Rcout);
+    }
+
     index = arma::sort_index(u);
     // arma::vec _w = w(index), _u = u(index);
 
@@ -35,17 +42,24 @@ arma::vec QRWMR(arma::mat const &x, arma::vec const &y, arma::vec b)
   return(b);
 }
 
-void QRWMR(arma::mat const &x, arma::vec const &y, arma::vec &b, arma::mat const &w, arma::vec const &totalWeights)
+void QRWMR(arma::mat const &x, arma::vec const &y, arma::vec &b, arma::mat const &w, arma::vec const &totalWeights, bool debugging)
 {
   int p = x.n_cols, n = x.n_rows;
   arma::vec t = y - x * b;
   arma::vec u(n, fill::none);
   arma::uvec index;
-  
+
   for(int m = 0; m < p; m++){
     t += x.col(m) * b(m);
     u = t/x.col(m);
 
+    if (debugging) {
+      Rcpp::Rcout << "Values of u before NaN replacement for column " << m << ":\n";
+      u.print(Rcpp::Rcout);
+    }
+
+    u.replace(datum::nan, 0);
+
     index = arma::sort_index(u);
 
 	double SUM = 0;

src/QR.h

@@ -4,7 +4,7 @@
 #include<RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 
-arma::vec QRWMR(arma::mat const &x, arma::vec const &y, arma::vec b);
-void QRWMR(arma::mat const &x, arma::vec const &y, arma::vec &b, arma::mat const &w, arma::vec const &totalWeights);
+arma::vec QRWMR(arma::mat const &x, arma::vec const &y, arma::vec b, bool debugging);
+void QRWMR(arma::mat const &x, arma::vec const &y, arma::vec &b, arma::mat const &w, arma::vec const &totalWeights, bool debugging);
 
-#endif
+#endif

src/RunCont.cpp

@@ -50,11 +50,11 @@ arma::vec RunCont_robust(arma::mat const &xc, arma::mat const &xg, arma::vec con
   arma::vec bold(p, fill::none), yc, yg; // bc = bc0, bg = bg0;
   arma::mat const wc = arma::abs(xc)/n;
   arma::vec const totalWeights = arma::sum(wc, 0).t();
-  
+
   while(count < 20){
 	yc = y - xg * bg;
 	// bc = QRWMR(xc, yc, bc);
-	QRWMR(xc, yc, bc, wc, totalWeights);
+	QRWMR(xc, yc, bc, wc, totalWeights, debugging);
 	yg = y - xc * bc;
 	bold = bg;
     if(method == 'n'){

src/RunSurv.cpp

@@ -24,7 +24,7 @@ arma::vec RunSurv_robust(arma::mat const &xc, arma::mat const &xg, arma::vec con
   while(count < 20){
 	yc = y - xg * bg;
 	// bc = QRWMR(xc, yc, bc);
-	QRWMR(xc, yc, bc, wc, totalWeights);
+	QRWMR(xc, yc, bc, wc, totalWeights, debugging);
 	yg = y - xc * bc;
 	bold = bg;
     if(method == 'n'){
@@ -62,7 +62,7 @@ void RunSurv_robust_warm(arma::mat const &xc, arma::mat const &xg, arma::vec con
   while(count < 20){
 	yc = y - xg * bg;
 	// bc = QRWMR(xc, yc, bc);
-	QRWMR(xc, yc, bc, wc, totalWeights);
+	QRWMR(xc, yc, bc, wc, totalWeights, false);
 	yg = y - xc * bc;
 	bold = bg;
     if(method == 'n'){