从邻接矩阵向 igraph 添加边权重

Question

给定一个单分 igraph 对象

G

和一个邻接矩阵

attrib

，仅包含 G 中的部分边的边属性 ，将属性添加到

G

的最有效方法是什么。

这是一个可重现的示例：

> set.seed(5)
> library(igraph)
> G <- erdos.renyi.game(10,.5,type="gnp")
> as_adjacency_matrix(G)  #Adjacency matrix for network

10 x 10 sparse Matrix of class "dgCMatrix"
                         
 [1,] . . . 1 1 . 1 1 1 1
 [2,] . . . 1 . . . 1 . .
 [3,] . . . 1 1 . 1 . 1 1
 [4,] 1 1 1 . 1 1 . . 1 1
 [5,] 1 . 1 1 . 1 . . . 1
 [6,] . . . 1 1 . . . 1 1
 [7,] 1 . 1 . . . . . 1 1
 [8,] 1 1 . . . . . . . .
 [9,] 1 . 1 1 . 1 1 . . .
[10,] 1 . 1 1 1 1 1 . . .

> attrib <- as_adjacency_matrix(G, sparse = FALSE)
> attrib[attrib==1] <- sample(c(0,1),sum(attrib),replace=TRUE)
> attrib  #Adjacency matrix containing attributes

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    1    1    0    0    0    1     0
 [2,]    0    0    0    0    0    0    0    1    0     0
 [3,]    0    0    0    0    0    0    1    0    1     1
 [4,]    0    1    1    0    1    1    0    0    0     0
 [5,]    1    0    1    0    0    0    0    0    0     1
 [6,]    0    0    0    1    0    0    0    0    1     0
 [7,]    0    0    1    0    0    0    0    0    0     1
 [8,]    1    0    0    0    0    0    0    0    0     0
 [9,]    1    0    1    1    0    1    0    0    0     0
[10,]    1    0    0    0    0    0    1    0    0     0

一种可能性是使

attrib

成为边缘列表，然后将它们在循环中一一添加。但是，我想一定有更好的选择。感谢您的任何想法。

Answer 1

输入数据

set.seed(5)
library(igraph)
n <- 10
G <- erdos.renyi.game(n, .5, type="gnp")
G <- simplify(G, remove.multiple = TRUE, remove.loops = TRUE)

attrib <- as_adjacency_matrix(G, sparse = FALSE)
attrib[attrib == 1] <- sample(c(0, 1),sum(attrib),replace = TRUE)
attrib  #Adjacency matrix containing attributes

在稀疏矩阵表示中使用三元组的解决方案

# Using the Matrix package.
# Create symmetric sparse matrix (M).
# Create vertex sequence (vp), x1, y1, x2, y2, ...
# Create a list of values (M@x)
library(Matrix)
M  <- as(attrib, "TsparseMatrix")
vp <- c(rbind(M@i, M@j)) + 1

# Convert vertex sequence to edge ids.
# Set edge attributes by edge id.
eids <- get.edge.ids(G, vp, directed=FALSE)
g2 <- set_edge_attr(G, "weight", index = eids, value=M@x)

# Show edges without weight.
E(g2)[which(is.na(E(g2)$weight))]
# + 5/23 edges from ad6a11e:
# [1] 1-- 7 4--10 5-- 6 6--10 7-- 9

g3 <- set_edge_attr(g2, name = "label", value = E(g2)$weight)
plot(g3)