From a56d6e547f0064837413334c2f75257599f82323 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Sat, 21 Sep 2024 21:40:59 +0200
Subject: [PATCH 1/2] removed for loops from get.incidence.dense

---
 R/conversion.R | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index ec548d0129..ddba5ee6bd 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -890,15 +890,14 @@ get.incidence.dense <- function(graph, types, names, attr) {
     recode[!types] <- seq_len(n1)
     recode[types] <- seq_len(n2)
 
-    for (i in seq(length.out = ecount(graph))) {
-      eo <- ends(graph, i, names = FALSE)
-      e <- recode[eo]
-      if (!types[eo[1]]) {
-        res[e[1], e[2]] <- edge_attr(graph, attr, i)
-      } else {
-        res[e[2], e[1]] <- edge_attr(graph, attr, i)
-      }
-    }
+    el <- as_edgelist(graph, names = FALSE)
+    idx <- types[el[, 1]]
+    el[, 1] <- recode[el[, 1]]
+    el[, 2] <- recode[el[, 2]]
+
+    tmp <- el[idx, 2:1]
+    el[idx, ] <- tmp
+    res[el] <- edge_attr(graph, attr)
 
     if (names && "name" %in% vertex_attr_names(graph)) {
       rownames(res) <- V(graph)$name[which(!types)]

From b68bef0b4192842a44b3d32de1089e2b86ec472c Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Wed, 9 Oct 2024 21:25:46 +0200
Subject: [PATCH 2/2] refactor and added comments to get.incidence.dense

---
 R/conversion.R | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index ddba5ee6bd..2129e22f8c 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -378,7 +378,6 @@ as_adjacency_matrix <- function(graph, type = c("both", "upper", "lower"),
 as_adj <- function(graph, type = c("both", "upper", "lower"),
                    attr = NULL, edges = deprecated(), names = TRUE,
                    sparse = igraph_opt("sparsematrices")) {
-
   lifecycle::deprecate_soft("2.1.0", "as_adj()", "as_adjacency_matrix()")
 
   as_adjacency_matrix(
@@ -887,16 +886,21 @@ get.incidence.dense <- function(graph, types, names, attr) {
     res <- matrix(0, n1, n2)
 
     recode <- numeric(vc)
+    # move from 1..n indexing to 1..n1 row indices for type == FALSE
+    # and 1..n2 col indices for type == TRUE
+    # recode holds the mapping [1..n] -> [1..n1,1..n2]
     recode[!types] <- seq_len(n1)
     recode[types] <- seq_len(n2)
 
     el <- as_edgelist(graph, names = FALSE)
     idx <- types[el[, 1]]
-    el[, 1] <- recode[el[, 1]]
-    el[, 2] <- recode[el[, 2]]
+    el[] <- recode[el]
 
-    tmp <- el[idx, 2:1]
-    el[idx, ] <- tmp
+    # switch order of source/target such that nodes with
+    # type == FALSE are in el[ ,1]
+    el[idx, ] <- el[idx, 2:1]
+    # el[ ,1] only holds values 1..n1 and el[ ,2] values 1..n2
+    # and we can populate the matrix
     res[el] <- edge_attr(graph, attr)
 
     if (names && "name" %in% vertex_attr_names(graph)) {