Re: [igraph] igraph-help Digest, Vol 117, Issue 1

[MikeS]

Tamas, thanks you for reply.
My code does not have syntactical error now.
But I concerned about the result, I think I have a logical error.

A modularity curve has the maximum value 0.4583 inside the steps'
range (on step with no.=18), but conductance curve has extremum 0 on
the right boundary.

> max(m)
[1] 0.4583333 # index =18
> max(con)
[1] 0 # index = 20

I am looking for a test dataset in order to check results.

library(igraph)
g <- make_graph( ~ A-B-C-D-A, E-A:B:C:D,
                      F-G-H-I-F, J-F:G:H:I,
                      K-L-M-N-K, O-K:L:M:N,
                      P-Q-R-S-P, T-P:Q:R:S,
                      B-F, E-J, C-I, L-T, O-T, M-S,
                      C-P, C-L, I-L, I-P)
gnc <- walktrap.community(g)
m <- vector()
con <- vector()
for (s in 0: nrow(gnc$merges)) {

memb <- cutat(gnc, steps=s)
m <- c(m, modularity (g, memb, weights=NULL))

g2<-make_clusters(g, memb)

  intra<-0
  extra<-0
    for(i in 1:length(E(g)))
        {
         ifelse(crossing(g2, g)[i]==FALSE, intra<-intra+1, extra<-extra+1)
    }
con <-c(con, extra/intra)

 }
windows()
par(mfrow=c(1:2))
plot(0:(length(m)-1), m, col="blue",xlab="Steps",ylab="Modularity")
plot(0:(length(con)-1), con, col="blue",xlab="Steps",ylab="Conductance")

Could someone please give me an idea where is error in my code?

2016-04-01 23:00 GMT+07:00  <address@hidden>:
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> Today's Topics:
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>    1. Re: Community detection based on conductance (MikeS)
>    2. Re: Community detection based on conductance (Tamas Nepusz)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 1 Apr 2016 08:50:31 +0700
> From: MikeS <address@hidden>
> To: address@hidden
> Subject: Re: [igraph] Community detection based on conductance
> Message-ID:
>         <address@hidden>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I would like to compare two partitioning network metric -- modularity
> and conductance -- step by step. Example code is shown below. Maximum
> modularity equal to
>
>> max(m)
> [1] 0.4583333
>
> library(igraph)
> g <- make_graph( ~ A-B-C-D-A, E-A:B:C:D,
>                       F-G-H-I-F, J-F:G:H:I,
>                       K-L-M-N-K, O-K:L:M:N,
>                       P-Q-R-S-P, T-P:Q:R:S,
>                       B-F, E-J, C-I, L-T, O-T, M-S,
>                       C-P, C-L, I-L, I-P)
> gnc <- walktrap.community(g)
>
> m <- vector()
> con <- vector()
> for (s in 0: nrow(gnc$merges)) {
>     memb <- cutat(gnc, steps=s)
>     m <- c(m, modularity (g, memb, weights=NULL))
>             intra<-0 # edge connects two nodes inside community
>            extra<-0 # edge connects two different communities
>         for(i in 1:length(E(g))) {
> #       ifelse(crossing(comm, g)[i]==FALSE, intra<- intra+1, extra<- extra+1)
>         }
> #   con <-c(con, intra/extra)
> }
>
> Could someone please give me an idea how to convert the vector 'memb'
> into community object 'comm'? Unfortunately, I don?t know how to pass
> the first argument to the crossing('comm', g).
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 1 Apr 2016 09:13:48 +0200
> From: Tamas Nepusz <address@hidden>
> To: Help for igraph users <address@hidden>
> Subject: Re: [igraph] Community detection based on conductance
> Message-ID:
>         <address@hidden>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
>> Could someone please give me an idea how to convert the vector 'memb'
> into community object 'comm'?
>
> make_clusters(graph, membership) seems to do the trick.
>
> T.
>
>
> On Fri, Apr 1, 2016 at 3:50 AM, MikeS <address@hidden> wrote:
>> Hello,
>>
>> I would like to compare two partitioning network metric -- modularity
>> and conductance -- step by step. Example code is shown below. Maximum
>> modularity equal to
>>
>>> max(m)
>> [1] 0.4583333
>>
>> library(igraph)
>> g <- make_graph( ~ A-B-C-D-A, E-A:B:C:D,
>>                       F-G-H-I-F, J-F:G:H:I,
>>                       K-L-M-N-K, O-K:L:M:N,
>>                       P-Q-R-S-P, T-P:Q:R:S,
>>                       B-F, E-J, C-I, L-T, O-T, M-S,
>>                       C-P, C-L, I-L, I-P)
>> gnc <- walktrap.community(g)
>>
>> m <- vector()
>> con <- vector()
>> for (s in 0: nrow(gnc$merges)) {
>>     memb <- cutat(gnc, steps=s)
>>     m <- c(m, modularity (g, memb, weights=NULL))
>>             intra<-0 # edge connects two nodes inside community
>>            extra<-0 # edge connects two different communities
>>         for(i in 1:length(E(g))) {
>> #       ifelse(crossing(comm, g)[i]==FALSE, intra<- intra+1, extra<- extra+1)
>>         }
>> #   con <-c(con, intra/extra)
>> }
>>
>> Could someone please give me an idea how to convert the vector 'memb'
>> into community object 'comm'? Unfortunately, I don?t know how to pass
>> the first argument to the crossing('comm', g).
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
>
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> End of igraph-help Digest, Vol 117, Issue 1
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