Hi Antoine, If I understand correctly, your last part of code is estimating the assortativity as if individuals that matches tend to links to the other that also matches and the same with the unmatches. This is correct?
I am some suggestions on how to calculate assortativity when we have a scalar characteristic with multiple values on each vertex, but I want to be sure if these suggestions could apply for your problem. Best regards, Fdo. El dom., 28 jul. 2019 a las 13:48, Chaillon, Antoine (<[email protected]>) escribió: > Dear Colleagues, > I am using igraph to explore assortativity of HLA profiles between linked > individuals (HIV) > My ‘problem’ is that for each HLA group (A, B or C), I have 2 values > associated with each vertex . > My goal is to determine if : > HLA A1 *OR* A2 are more likely to be ‘assortative’ in the network > HLA B1 *OR* B2 are more likely to be ‘assortative’... > HLA C1 *OR* C2 are more likely to be ‘assortative’... > > For now, I compare it to a random distribution. > For example with HLA C (C1 or C2), I have 28 unique HLAC profile. > In a network with 286 vertices, First I calculate the rdm_assortativity as > follow: > RandomSample <- > sample(c(1,2,5,4,6,7,8,9,10,3,11,12,14,13,16,17,15,18,19,20,21,22,23,24,25,26,27,28), > 286, replace=TRUE) ## my guess is that the dimension is incorrect because > it does not take into account the 2 possibilities (C1 and C2) > rdm_assortativity=assortativity_nominal(graph=ALLEDGES2, > types=RandomSample, directed = F) > > Next, I want to determine the *observed* assortativity. What would you > suggest? > For now, I manually created an additional column ‘HLAC_match’ with 1 for > ‘match’ and 2 for ’no match’ and then calculate the assortativity as follow: > assortativity_nominal(graph=ALLEDGES2, types=HLAATTRIBUTES$HLAC_match, > directed = F) # where ALLEDGES is my edge list > > Does that make sense? > Any thoughts? > thank you in advance! > a > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help >
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