[英]Converting all_shortest_paths vpaths to epaths in R igraph
[英]Extracting information from the `all_shortest_paths` function from `igraph` package in R
對於此示例圖:
set.seed(1)
g <- make_chordal_ring(15, matrix(c(3, 12, 4, 7, 8, 11), nr = 2))
k <- Vectorize(all_shortest_paths, "from", F)(g, V(g), 7)
我們擁有所有最短路徑,從圖中的任何給定節點開始,到節點7(參考節點)結束。 我要計算的是從節點X到節點7的最短路徑中節點Y出現的次數。
如果我表示從節點1到節點7的最短路徑經過n(1,2,7)的數量,而從節點1到節點7的最短路徑總數由n(1,7)表示,想要一種生成如下表的方法:
例如,如果我們看一下k的輸出,我真的會堅持這樣做:
> k[[1]][1]
$res
$res[[1]]
+ 3/15 vertices:
[1] 1 4 7
我不知道如何隔離路徑1,4,7並將其計入n(1,4,7)
我會去一個簡單的循環:
# initialize your matrix with all zeros
m <- matrix(0,nrow=vcount(g),ncol=vcount(g)+1)
# iterate over elements of k
for(fromVertex in 1:length(k)){
# iterate over res entry of each element of k
for(path in k[[fromVertex]]$res){
# path is a vertex sequence, same type as V(g),
# calling as.integer we get the vertices indexes inside the sequence
verticesOfPath <- as.integer(path)
# we exclude the first and the last vertex (from,to)
innerVertices <- verticesOfPath[c(-1,-length(verticesOfPath))]
if(length(innerVertices) > 0){
# this is not a direct path
m[verticesOfPath[1],innerVertices] <- m[verticesOfPath[1],innerVertices] + 1
}
# add 1 to the last column
m[verticesOfPath[1],ncol(m)] <- m[verticesOfPath[1],ncol(m)] + 1
}
}
結果:
> m
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
[2,] 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
[3,] 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
[4,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[5,] 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 2
[6,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[7,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[8,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[9,] 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 2
[10,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[11,] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1
[12,] 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
[13,] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1
[14,] 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
[15,] 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
如果頂點具有名稱屬性,則可以將它們設置為矩陣的行名和列名:
rownames(m) <- V(g)$name
colnames(m) <- c(V(g)$name,'TOT')
> m
A B C D E F G H I J K L M N O TOT
A 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
B 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
C 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
E 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 2
F 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
H 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
I 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 2
J 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
K 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1
L 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
M 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1
N 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1
O 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
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