Hi, In igraph I have created a network with weighted edges, and I have set the vertex attributes.
I now want to use this graph object to calculate the assortativity of the network. The problem is that some of my vertices are labeled NA (as we do not have the attribute information for those nodes). igraph will not calculate the assortativity with the NA's present. I have tried na.omit(x) but this does not work. Can someone suggest how I can remove the NA's from the g to be able to calculate the assortaitivity? My code and the vertex output is as follows: library(igraph) accumul_d123.copy[,1]=as.character(accumul_d123.copy[,1]) accumul_d123.copy[,2]=as.character(accumul_d123.copy[,2]) accumul_d123.copy=as.matrix(accumul_d123.copy) g=graph.edgelist(accumul_d123.copy[,1:2],directed=FALSE) E(g)$weight=as.numeric(accumul_d123.copy[,3]) adj=get.adjacency(g,attr='weight') adj g # import vaccination status file to label the nodes in g g123 <- set.vertex.attribute(g,"vaccination", index=vacc_status_variant$V1, value=vacc_status_variant$V2) #labeled 123 as accumulated for days 1,2&3 get.vertex.attribute(g123, "vaccination") #vertex attributes [1] 1 NA 1 1 1 1 2 2 NA NA NA 2 2 NA 1 NA 1 1 NA 2 1 1 NA NA NA 1 1 1 2 NA 1 NA 1 [34] NA 1 2 2 1 1 1 1 NA NA 2 1 2 1 2 NA 1 NA 1 NA 1 1 1 2 NA 1 1 1 1 2 1 2 1 [67] 2 NA NA NA 2 1 2 NA NA NA NA 2 2 1 NA 1 NA NA 2 NA 1 NA 2 2 1 NA NA NA NA 2 1 1 NA [100] 2 1 1 2 NA NA 1 1 NA NA 1 NA 1 2 NA 2 NA 1 2 2 NA 2 1 NA NA NA 1 1 NA 2 NA 2 1 [133] 2 NA NA 2 2 1 1 2 2 2 NA NA 2 NA 2 2 2 NA 1 1 NA NA 2 1 NA 1 1 1 NA NA NA NA 1 [166] NA NA 2 NA 1 2 2 1 1 1 1 NA 1 2 NA 1 NA 1 NA 2 NA 2 1 1 2 2 1 2 1 NA 1 NA 2 [199] 1 1 2 1 1 1 NA NA 1 2 NA 1 NA 1 1 2 NA 2 2 NA 1 1 2 1 NA NA NA 2 NA 2 NA 2 2 [232] NA NA 2 NA 2 1 NA 1 NA 1 NA 1 NA NA 1 NA NA 1 NA 2 NA NA 1 1 2 1 NA 2 1 NA 2 1 NA [265] NA 2 NA NA 1 NA 1 NA NA 2 NA NA NA 1 1 2 1 NA 1 1 NA 1 NA 2 NA NA NA 2 1 2 NA 2 1 [298] NA 1 1 NA 1 2 NA NA 1 NA 2 NA NA 1 NA NA 1 1 1 1 NA 1 2 2 NA assortativity(g123,V(g123)$vaccination,directed=F) # calculate assortativity for all cpr's [1] NA Thanks _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
