How do I calculate weighted degree distributions with igraph in R?
题
Consider a dataframe df
where the first two columns are node pairs and successive columns V1
, V2
, ..., Vn
represent flows between the nodes (potentially 0, implying no edge for that column's network). I would like to conduct analysis on degree, community detection, and other network measures using the flows as weights.
Then to analyze the graph with respect to the weights in V1
I do:
# create graph and explore unweighted degrees with respect to V1
g <- graph.data.frame( df[df$V1!=0,] )
qplot(degree(g))
x <- 0:max(degree(g))
qplot(x,degree.distribution(g))
# set weights and explore weighted degrees using V1
E(g)$weights <- E(g)$V1
qplot(degree(g))
The output from the third qplot is no different than the first. What am I doing wrong?
Update:
So graph.strength
is what I am looking for, but graph.strength(g)
in my case gives standard degree output followed by:
Warning message:
In graph.strength(g) :
At structural_properties.c:4928 :No edge weights for strength calculation,
normal degree
I must be setting the weights incorrectly, is it not sufficient to do E(g)$weights <- E(g)$V1
and why can g$weights
differ from E(g)$weights
?
解决方案
The function graph.strength
can be given a weights vector with the weights
argument. I think what is going wrong in your code is that you should call the weights attribute E(g)$weight
not E(g)$weights
.
其他提示
I created an equivalent degree.distribution
function for weighted graphs for my own code by taking the degree.distribution
code and making one change:
graph.strength.distribution <- function (graph, cumulative = FALSE, ...)
{
if (!is.igraph(graph)) {
stop("Not a graph object")
}
# graph.strength() instead of degree()
cs <- graph.strength(graph, ...)
hi <- hist(cs, -1:max(cs), plot = FALSE)$density
if (!cumulative) {
res <- hi
}
else {
res <- rev(cumsum(rev(hi)))
}
res
}