problems with assortativity coefficient

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problems with assortativity coefficient

Rui Carvalho-2

Hi,

 

I'm trying to compute Newman's assortativity coefficient with graph-tool, but I'm getting unexpected high values of r.

 

Here's a test:

graph-tool --correlated-configurational-model="N=20000,inv_pjk_ceil=\"(inv_poisson(p,5),inv_poisson(r,5))\",progress" \

--save graph.xml

 

graph-tool --load graph.xml --assortativity-coefficient="total-degree"

 

this is what I get:

 assortativity coefficient (total-degree)

0.2105496706333980228                0.0036187517305024605174

 

The assortativity value above should be very close to zero as the network is uncorrelated, but it’s reasonably large.

 

Also, when I try:

graph-tool --load graph.xml --scalar-assortativity-coefficient="total-degree"

 

graph-tool crashes:

Traceback (most recent call last):

  File "/usr/bin/graph-tool", line 494, in <module>

    _main()

  File "/usr/bin/graph-tool", line 470, in _main

    run(parsed_options)

  File "/usr/bin/graph-tool", line 356, in run

    output_file = opt[0].output_file

AttributeError: OptionMask instance has no attribute 'output_file'

 

I'm running graph-tool 1.2.0devel (commit 8b98b8c6, Sun Jul 20 11:46:39 2008 +0200)

 

Am I missing something obvious?

 

many thanks,

Rui

 

 

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Re: problems with assortativity coefficient

Tiago de Paula Peixoto
Hi.

The problem you reported with the second option is now fixed in git. I
however cannot see high values of assortativity:

graph-tool --correlated-configurational-model="N=20000,inv_pjk_ceil=\"lambda p,r: (inv_poisson(p,5), inv_poisson(r,5))\"" --assortativity-coefficient="total-degree" --scalar-assortativity-coefficient="total-degree"

# assortativity coefficient (total-degree)
0.089740322372172054433 0.00391706558657752002

# scalar assortativity coefficient (total-degree)
0.0024758906274759966311 0.0031450246340287649899

Please test with the version now in git, and see if you still see the
same problem.

Cheers,
Tiago

On 11/17/2008 01:28 AM, Rui Carvalho wrote:

> Hi,
>
>  
>
> I'm trying to compute Newman's assortativity coefficient with graph-tool,
> but I'm getting unexpected high values of r.
>
>  
>
> Here's a test:
>
> graph-tool
> --correlated-configurational-model="N=20000,inv_pjk_ceil=\"(inv_poisson(p,5)
> ,inv_poisson(r,5))\",progress" \
>
> --save graph.xml
>
>  
>
> graph-tool --load graph.xml --assortativity-coefficient="total-degree"
>
>  
>
> this is what I get:
>
>  assortativity coefficient (total-degree)
>
> 0.2105496706333980228                0.0036187517305024605174
>
>  
>
> The assortativity value above should be very close to zero as the network is
> uncorrelated, but it's reasonably large.
>
>  
>
> Also, when I try:
>
> graph-tool --load graph.xml
> --scalar-assortativity-coefficient="total-degree"
>
>  
>
> graph-tool crashes:
>
> Traceback (most recent call last):
>
>   File "/usr/bin/graph-tool", line 494, in <module>
>
>     _main()
>
>   File "/usr/bin/graph-tool", line 470, in _main
>
>     run(parsed_options)
>
>   File "/usr/bin/graph-tool", line 356, in run
>
>     output_file = opt[0].output_file
>
> AttributeError: OptionMask instance has no attribute 'output_file'
>
>  
>
> I'm running graph-tool 1.2.0devel (commit 8b98b8c6, Sun Jul 20 11:46:39 2008
> +0200)
>
>  
>
> Am I missing something obvious?
>
>  
>
> many thanks,
>
> Rui
>
>  
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> graph-tool mailing list
> [hidden email]
> http://lists.forked.de/mailman/listinfo/graph-tool


--
Tiago de Paula Peixoto <[hidden email]>

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Re: problems with assortativity coefficient

Rui Carvalho-2
Hi,

After installing the new ver I get the same results as you do. However, I
get an error when I type the following (taken from the documentation):

graph-tool
--correlated-configurational-model="N=20000,inv_pjk_ceil=\"(inv_poisson(p,5)
,inv_poisson(r,5))\",progress" \--save graph.xml.bz2

returns:
adding vertices: 1 of 20000 (0%)graph-tool: error during evaluation of
command
--correlated-configurational-model=N=20000,inv_pjk_ceil="(inv_poisson(p,5),i
nv_poisson(r,5))",progress: <lambda>() takes no arguments (2 given)


My understanding is that the documentation is somehow partially out-of-date
due to the ongoing upgrade of graph-tool, but I just wanted to check that
this is the reason for the error I'm getting.

Cheers,
Rui

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Tiago de Paula Peixoto
Sent: 18 November 2008 19:55
To: Main discussion list for the graph-tool project
Subject: Re: [graph-tool] problems with assortativity coefficient

Hi.

The problem you reported with the second option is now fixed in git. I
however cannot see high values of assortativity:

graph-tool --correlated-configurational-model="N=20000,inv_pjk_ceil=\"lambda
p,r: (inv_poisson(p,5), inv_poisson(r,5))\""
--assortativity-coefficient="total-degree"
--scalar-assortativity-coefficient="total-degree"

# assortativity coefficient (total-degree)
0.089740322372172054433 0.00391706558657752002

# scalar assortativity coefficient (total-degree)
0.0024758906274759966311 0.0031450246340287649899

Please test with the version now in git, and see if you still see the
same problem.

Cheers,
Tiago

On 11/17/2008 01:28 AM, Rui Carvalho wrote:

> Hi,
>
>  
>
> I'm trying to compute Newman's assortativity coefficient with graph-tool,
> but I'm getting unexpected high values of r.
>
>  
>
> Here's a test:
>
> graph-tool
>
--correlated-configurational-model="N=20000,inv_pjk_ceil=\"(inv_poisson(p,5)

> ,inv_poisson(r,5))\",progress" \
>
> --save graph.xml
>
>  
>
> graph-tool --load graph.xml --assortativity-coefficient="total-degree"
>
>  
>
> this is what I get:
>
>  assortativity coefficient (total-degree)
>
> 0.2105496706333980228                0.0036187517305024605174
>
>  
>
> The assortativity value above should be very close to zero as the network
is

> uncorrelated, but it's reasonably large.
>
>  
>
> Also, when I try:
>
> graph-tool --load graph.xml
> --scalar-assortativity-coefficient="total-degree"
>
>  
>
> graph-tool crashes:
>
> Traceback (most recent call last):
>
>   File "/usr/bin/graph-tool", line 494, in <module>
>
>     _main()
>
>   File "/usr/bin/graph-tool", line 470, in _main
>
>     run(parsed_options)
>
>   File "/usr/bin/graph-tool", line 356, in run
>
>     output_file = opt[0].output_file
>
> AttributeError: OptionMask instance has no attribute 'output_file'
>
>  
>
> I'm running graph-tool 1.2.0devel (commit 8b98b8c6, Sun Jul 20 11:46:39
2008

> +0200)
>
>  
>
> Am I missing something obvious?
>
>  
>
> many thanks,
>
> Rui
>
>  
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> graph-tool mailing list
> [hidden email]
> http://lists.forked.de/mailman/listinfo/graph-tool


--
Tiago de Paula Peixoto <[hidden email]>
_______________________________________________
graph-tool mailing list
[hidden email]
http://lists.forked.de/mailman/listinfo/graph-tool


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Re: problems with assortativity coefficient

Tiago de Paula Peixoto
On 11/21/2008 06:27 PM, Rui Carvalho wrote:

> Hi,
>
> After installing the new ver I get the same results as you
> do. However, I get an error when I type the following (taken from the
> documentation):
>
> graph-tool
> --correlated-configurational-model="N=20000,inv_pjk_ceil=\"(inv_poisson(p,5)
> ,inv_poisson(r,5))\",progress" \--save graph.xml.bz2
>
> returns:
> adding vertices: 1 of 20000 (0%)graph-tool: error during evaluation of
> command
> --correlated-configurational-model=N=20000,inv_pjk_ceil="(inv_poisson(p,5),i
> nv_poisson(r,5))",progress: <lambda>() takes no arguments (2 given)
>
>
> My understanding is that the documentation is somehow partially
> out-of-date due to the ongoing upgrade of graph-tool, but I just
> wanted to check that this is the reason for the error I'm getting.
Yes, there is a discrepancy with the documentation. You should do:
"lambda p,r: (inv_poisson(p,5), inv_poisson(r,5))".

All this will be largely deprecate with the new version of graph-tool as
(purely) a python library. It should be coming out "real soon now"™, and
will include up-to-date documentation.

Cheers,
Tiago

--
Tiago de Paula Peixoto <[hidden email]>


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