[igraph] Re: igraph-help Digest, Vol 30, Issue 1

[Aisan Kazerani]

Hi Gabor,

Thanks for your advice, but there's still a RUNTIME error after I run my
weighted betweenness program, saying:

R FOR WINDOWS GUI FRONT-END HAS ENCOUNTERED A PROBLEM AND NEEDS TO CLOSE.
WE ARE SORRY FOR THE ENCONVENIENCE.

I have entered my graph manually using the graph command,not with pajek
file this time. My graph has 57 vertices and 82 edges. Would you please
help me out of this!!

Thanks a lot..
Aisan






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> Today's Topics:
>
>    1. igraph 0.6 (Aisan Kazerani)
>    2. igraph 0.6 (Aisan Kazerani)
>    3. Re: igraph 0.6 ( G?bor Cs?rdi )
>    4. Re: MCL Algorithm ( G?bor Cs?rdi )
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 01 Jan 2009 11:28:11 +1100 (EST)
> From: Aisan Kazerani <address@hidden>
> Subject: [igraph] igraph 0.6
> To: address@hidden
> Message-ID:
>       <address@hidden>
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear sir,
>
> Does igraph package 0.6 work on Linux only, or does it work on windows as
> well, because it doesn't consider the weights of edges for calculating
> betweenness under R.
>
> Thanks.
> Aisan Kazerani
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 01 Jan 2009 12:11:47 +1100 (EST)
> From: Aisan Kazerani <address@hidden>
> Subject: [igraph] igraph 0.6
> To: address@hidden
> Message-ID:
>       <address@hidden>
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear sir,
>
> Does igraph package 0.6 work on Linux only, or does it work on windows as
> well, because it doesn't consider the weights of edges for calculating
> betweenness under R in windows. My input is in pajek format with edge
> weights, and these are my commands. But there is no difference between the
> results of weighted betweenness and unweighted one.
>
> r <- read.graph ("test1.net", format="pajek")
> betweenness(r)
>
> Thanks.
> Aisan Kazerani
>
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 1 Jan 2009 10:42:55 +0100
> From: " G?bor Cs?rdi " <address@hidden>
> Subject: Re: [igraph] igraph 0.6
> To: "Help for igraph users" <address@hidden>,         "Aisan
>       Kazerani" <address@hidden>
> Message-ID:
>       <address@hidden>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Thu, Jan 1, 2009 at 2:11 AM, Aisan Kazerani
> <address@hidden> wrote:
>> Dear sir,
>>
>> Does igraph package 0.6 work on Linux only,
>
> No. Actually, if you have downloaded
> http://cneurocvs.rmki.kfki.hu/igraph/download/igraph_0.6.zip
> that is windows only.
>
>> or does it work on windows as
>> well, because it doesn't consider the weights of edges for calculating
>> betweenness under R in windows. My input is in pajek format with edge
>> weights, and these are my commands. But there is no difference between
>> the
>> results of weighted betweenness and unweighted one.
>>
>> r <- read.graph ("test1.net", format="pajek")
>> betweenness(r)
>
> Possible mistakes:
> 1) your test1.net file does not have weights (check the file in an
> editor),
> 2) all weights in your file are the same (check the file in an editor),
> 3) you are not using the 0.6 version of igraph (check the version you are
> using,
>     e.g. with library(help=igraph) )
>
> It definitely works for me (or gives different results in the weighted
> case at least), both on Linux and Windows, I've just tried it:
>
>> library(igraph)
>> g <- graph.ring(10)
>> betweenness(g)
>  [1] 8 8 8 8 8 8 8 8 8 8
>> E(g)$weight <- runif(ecount(g))
>> betweenness(g)
>  [1]  4  6  8 10 12 12 11  9  7  5
>
> Best,
> G.
>
>> Thanks.
>> Aisan Kazerani
>>
>>
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>
>
>
> --
> Gabor Csardi <address@hidden>     UNIL DGM
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 1 Jan 2009 11:14:12 +0100
> From: " G?bor Cs?rdi " <address@hidden>
> Subject: Re: [igraph] MCL Algorithm
> To: "Help for igraph users" <address@hidden>
> Message-ID:
>       <address@hidden>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks Chris, I've added your code to the (experimental and rather
> empty) igraph wiki:
> http://igraph.wikidot.com/community-detection-in-python
> I hope you don't mind.
>
> G.
>
> On Wed, Dec 31, 2008 at 5:11 PM, Chris Wj <address@hidden> wrote:
>> Well we certainly appreciate all the work you put in to the library.
>>
>> Quick Python code snippet I whipped up to test using MLC with igraph
>> (uses
>> subprocess and pipes):
>>
>> import igraph
>>
>> def igraph_to_mcl_matrix():
>>     from subprocess import Popen, PIPE
>>     from cStringIO import StringIO
>>     G1 = igraph.Graph(n=3)
>>     G1.add_edges(((0,1),(0,2),(1,2)))
>>     mcifile = StringIO()
>>     mclheader = (
>>         ("\n(mclheader\n"),
>>         ("mcltype matrix\n"),
>>         ( "dimensions %sx%s\n)\n" % (G1.vcount(), G1.vcount()) ),
>>         ("(mclmatrix\n"),
>>         ("begin\n")
>>     )
>>     mcifile.writelines(mclheader)
>>     for v in G1.vs:
>>         mcifile.write(str(v.index) + " ")
>>         for n in G1.neighbors(v.index):
>>             mcifile.write(str(n) + " ")
>>         mcifile.write(" $\n")
>>     mcifile.write(")\n")
>>     mcifile.seek(0)
>>     cmd = "mcl - -o -"
>>     p = Popen(cmd, stdout=PIPE, stdin=PIPE, stderr=PIPE)
>>     sout,serr = p.communicate(mcifile.read())
>>     p.wait()
>>     #print "return code: %i\n" % p.returncode
>>     if p.returncode==0 and len(sout)>0:
>>         lines = sout.splitlines()
>>         idx_begin = lines.index("begin")+1
>>         idx_end = lines[idx_begin:].index(")")+idx_begin
>>         for line in lines[idx_begin:idx_end]:
>>             print line
>>
>> I used StringIO because I originally was using file IO before piping and
>> it
>> was easier to switch the code back and forth between string and file
>> objects.
>>
>> On Wed, Dec 31, 2008 at 3:43 AM, G�bor Cs�rdi <address@hidden> wrote:
>>>
>>> Chris,
>>>
>>> this is always a difficult decision, the main problem is, that it is
>>> not easy to do it in a way that allows us to include future updates as
>>> well. Furthermore we will need to maintain the code in the future and
>>> that is sometimes problematic, a large portion of portability problems
>>> we get are due to some 3rd party C++ codes we put into igraph....
>>>
>>> We already include many smaller and bigger pieces of software, e.g.
>>> the walktrap, the spinglass community finding algorithms, parts of
>>> ARPACK, LAPACK and BLAS, the BLISS graph isomorphism library, etc.
>>>
>>> Maybe I am just frustrated because I have been trying to repair the
>>> igraph version of ARPACK for a couple of days now....
>>>
>>> But actually the MCL code looks pretty good. So we will see. Thanks for
>>> the tip.
>>>
>>> Best,
>>> Gabor
>>>
>>> On Tue, Dec 30, 2008 at 11:20 PM, Chris Wj <address@hidden> wrote:
>>> > I have been using MCL lately and before working on a way to export
>>> > igraph in
>>> > MCL matrix format, I was looking to see if there was any further
>>> > thoughts on
>>> > including this library in igraph. I searched the archives and found
>>> that
>>> > Tamas said something about possibly including MCL in igraph.
>>> > For now, I will probably just exec it (popen) to test it.
>>> >
>>> > MCL: http://www.micans.org/mcl/
>>> >
>>> > _______________________________________________
>>> > igraph-help mailing list
>>> > address@hidden
>>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Gabor Csardi <address@hidden>     UNIL DGM
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
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>
>
>
> --
> Gabor Csardi <address@hidden>     UNIL DGM
>
>
>
>
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> End of igraph-help Digest, Vol 30, Issue 1
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