I am very sorry for this silly mistake. The last question though: when I have discrete categories, and I am using gt.assortativity, what role does the parameter "deg" play? The comment in the source code says: "this will calculate the assortativity coefficient, based on the property pointed by 'deg' ". What does this mean? Thank you Snehal On Fri, Oct 6, 2017 at 7:15 PM, Tiago de Paula Peixoto <tiago@skewed.de> wrote:
On 06.10.2017 14:05, Snehal Shekatkar wrote:
Of course, the degree is a discrete variable. I said we treat it as a continuous variable because we don't categorize the degree values like we do for a gender. For example, we don't treat degree values 25 and 26 as two different categories. (Formula 7.82 in Newman's book).
You are confusing "continuous" with "scalar". Degrees are discrete _scalar_ values, that are better characterized via the _scalar_ assortativity coefficient, rather than the plain assortativity coefficient (which is not invalid, only less useful).
I am discarding repetitions because I wanted to treat unique degree values as discrete types. For example, to study mixing by genders, I will have first to find out the unique gender values. What is wrong with this?
Sorry, I misunderstood your code. It is actually wrong in other places. What you wanted to compute was:
g = gt.collection.data['karate']
# Unique degree values or types deg_vals = list(set([v.out_degree() for v in g.vertices()])) n = len(deg_vals)
e = np.zeros(n) # fraction of edges that connect similar vertices a = np.zeros(n) # fraction of edges connected to a vertx of a given type
for v in g.vertices(): for nbr in v.out_neighbours(): a[deg_vals.index(v.out_degree())] += 1 if v.out_degree() == nbr.out_degree(): e[deg_vals.index(v.out_degree())] += 1
a /= 2 * g.num_edges() e /= 2 * g.num_edges() r = (sum(e)-sum(a**2))/(1-sum(a**2))
print(r) print(gt.assortativity(g, deg = 'out'))
Which yields:
-0.0777450257922 (-0.07774502579218864, 0.024258508125118667)
(Note that it is not up to me to show how your calculation is wrong; it is up to you to show that it is right.)
-- Tiago de Paula Peixoto <tiago@skewed.de>
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-- Snehal M. Shekatkar Pune India