Re: [igraph] Calculating average shortest path

[Claudia Muller-Birn]

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
>> 
>> 
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>> 
> 
> 
> 
> -- 
> Gabor Csardi <address@hidden>     UNIL DGM