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Re: [igraph] Calculating average shortest path
From: |
Claudia Muller-Birn |
Subject: |
Re: [igraph] Calculating average shortest path |
Date: |
Sun, 6 Mar 2011 10:15:47 +0100 |
Hi Gabor,
Okay, great. I understand.
Thank you!
Claudia
On Mar 6, 2011, at 1:27 AM, Gábor Csárdi wrote:
> Hi Claudia,
>
> when you use shortest.path(), you also count the paths from each
> vertex to itself, this is why the result is different. These self
> paths (always of length zero) are not counted in
> average.shortest.paths().
>
> undiag <- function(x) { diag(x) <- NA; x[is.infinite(x)] <- NA ;
> na.omit(as.vector(x)) }
> mean(undiag(shortest.paths(g1)))
> mean(undiag(shortest.paths(g2, mode="out")))
>
> Best,
> Gabor
>
> On Sat, Mar 5, 2011 at 5:53 PM, Claudia Muller-Birn <address@hidden> wrote:
>> Dear all,
>>
>> I have a rather simple question regarding calculating the average shortest
>> path length. There are actually to ways calculating it and I am wondering
>> why I get two different results. Here is my toy example:
>>
>>> g1 <- graph( c( 0,1, 1,2, 2,1, 2,3 ), directed=FALSE )
>>> g2 <- graph( c( 0,1, 1,2, 2,1, 2,3 ), directed=TRUE )
>>
>> First possibility to calculate the average shortest path (or is it just one
>> path???)
>>> average.path.length(g1, directed=FALSE)
>> [1] 1.666667
>>> average.path.length(g2, directed=TRUE)
>> [1] 1.571429
>>
>> Second possibility would be by just calling the mean
>>> sp1 <- shortest.paths(g1)
>>> mean(sp1,na.rm=TRUE)
>> [1] 1.25
>>> sp2 <- shortest.paths(g2, v=V(g2), mode='out')
>>> sp2[is.infinite(sp2)]<-NA
>>> mean(sp2,na.rm=TRUE)
>> [1] 1
>>
>> In my opinion, the second way to calculate the average shortest paths makes
>> much more sense but then I am wondering about the meaning and calculation of
>> the first possibility based on average.path.length. How is the latter
>> function implemented or do I miss some settings?
>>
>> Thank you very much for any help or idea.
>>
>> Best,
>> Claudia
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>
>
>
> --
> Gabor Csardi <address@hidden> UNIL DGM