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Today's Topics:
1. Clusters in Graph (Surendar Swaminathan)
2. How to do degree distribution fitting? (=?gb2312?B?zfXWvr2t?=)
3. Installation of igraph on ubuntu 9.10 amd64 (Lorenzo Isella)
4. Creating a bipartite graph (Mouly)
5. Re: Creating a bipartite graph (Tamas Nepusz)
6. Re: Clusters in Graph (Tamas Nepusz)
7. Re: Installation of igraph on ubuntu 9.10 amd64 (Tamas Nepusz)
----------------------------------------------------------------------
Message: 1
Date: Sun, 1 Nov 2009 12:24:53 -0800
From: Surendar Swaminathan <address@hidden>
Subject: [igraph] Clusters in Graph
To: address@hidden, Help for igraph users
<address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=ISO-8859-1
Hello All,
I am using Igraph for R version 2.9. What I have is a Node Node
information of a fragmented graph. The whole graph object is made up
of multiple clusters.The highest cluster in the graph is 335 nodes and
the second highest is 219 nodes and the third is 178 and it keeps
going to n. Is there any way in Igraph I would be able to output all
the the clusters from one single graph object.
As of now I am doing them manually.Is there a way I can do it with one
single graph object using Igraph code.
Thank you very much for the help.
Surendar
------------------------------
Message: 2
Date: Mon, 2 Nov 2009 13:37:23 +0800
From: "=?gb2312?B?zfXWvr2t?=" <address@hidden>
Subject: [igraph] How to do degree distribution fitting?
To: "igraph-help" <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset="gb2312"
Dear All,
I am a rookie now.
I want to know how do the degree distribution (truncated power law
not power law) fitting?
Thanks a lot!
------------------------------
Message: 3
Date: Mon, 2 Nov 2009 15:44:07 +0100
From: Lorenzo Isella <address@hidden>
Subject: [igraph] Installation of igraph on ubuntu 9.10 amd64
To: address@hidden
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=ISO-8859-1
Dear All,
I am trying to install the igraph library on my ubuntu 9.10 system. I
did the procedure which used to work for me in the past
$ sudo apt-get source igraph
$ cd igraph-0.5.2/
$ sudo dpkg-buildpackage -rfakeroot
but something went wrong as I had the following output
dpkg-deb: building package `libigraph' in `../
libigraph_0.5.2_amd64.deb'.
dpkg-deb: building package `libigraph-dev' in
`../libigraph-dev_0.5.2_amd64.deb'.
signfile igraph_0.5.2.dsc
gpg: WARNING: unsafe ownership on configuration file
`/home/lorenzo/.gnupg/gpg.conf'
gpg: skipped "Tamas Nepusz <address@hidden>": secret key not
available
gpg: [stdin]: clearsign failed: secret key not available
dpkg-genchanges >../igraph_0.5.2_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-buildpackage: full upload; Debian-native package (full source
is included)
dpkg-buildpackage: warning: Failed to sign .dsc and .changes file
And no Debian package was produced.
What am I doing wrong? I never had such a problem with signatures in
the past.
Many thanks
Lorenzo
------------------------------
Message: 4
Date: Mon, 2 Nov 2009 09:57:21 -0500
From: Mouly <address@hidden>
Subject: [igraph] Creating a bipartite graph
To: address@hidden
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
I'm trying to create a bipartite graph (one group is a numeric ids,
and the
other is a string) with the following command:
g <- graph.bipartite(rep(0:1,10),c('1','a','2','c','3','a',
1,'c','4','d'))
I get the error message
Error in graph.bipartite(rep(0:1, 10), c("1", "a", "2", "c", "3",
"a", :
At bipartite.c:456 : Invalid edges, not a bipartite graph, Invalid
value
In addition: Warning message:
In graph.bipartite(rep(0:1, 10), c("1", "a", "2", "c", "3", "a", :
NAs introduced by coercion
Can someone show me the correct way to create a bipartite graph? I
don't
understand how igraph validates that the edges do belong to different
groups.
-mouly
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Message: 5
Date: Mon, 2 Nov 2009 15:46:09 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] Creating a bipartite graph
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
I'm trying to create a bipartite graph (one group is a numeric ids,
and the
other is a string) with the following command:
g <- graph.bipartite(rep(0:1,10),c('1','a','2','c','3','a',
1,'c','4','d'))
Note that igraph works with numeric vertex IDs starting from zero, not
with string IDs. This applies to graph.bipartite() as well. Since you
are constructing a graph with 20 vertices, your vertices will have IDs
from zero to 19. Moreover, vertices 0, 2, 4, ..., 16, 18 will be of
type 0,
while vertices 1, 3, 5, ..., 17 and 19 will be of type 1, according
to the
type vector you supplied. In the second argument, you will have to
pass
something like this:
c(0, 5, 1, 6, 2, 7, 3, 8, 4, 9)
This means that the first edge will go from vertex 0 to vertex 5, the
second will go from vertex 1 to vertex 6 and so on:
g <- graph.bipartite(rep(0:1, 10), c(0,5,1,6,2,7,3,8,4,9))
g
Vertices: 20
Edges: 5
Directed: FALSE
Edges:
[0] 0 -- 5
[1] 1 -- 6
[2] 2 -- 7
[3] 3 -- 8
[4] 4 -- 9
Also note that from igraph's point of view, a bipartite graph is
simply
a graph with a "type" attribute that describes the vertex types, and
igraph functions working with bipartite graphs only will check this
attribute. However, there's nothing that stops you from adding an edge
between two vertices of the same type using add.edges().
--
Tamas
------------------------------
Message: 6
Date: Mon, 2 Nov 2009 15:51:22 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] Clusters in Graph
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
Hi Surendar,
If you are looking for the connected components of a graph, check the
help page for the following commands:
?clusters
?decompose.graph
"clusters" will give you a numeric vector which contains N elements (N
is the number of nodes in your graph). Each element of this vector is
the cluster index of the corresponding node; nodes in cluster X will
have X in the corresponding position in the membership vector.
"decompose.graph" will take the original graph and return a list of
graphs, each corresponding to one component of your original graph.
--
Tamas
------------------------------
Message: 7
Date: Mon, 2 Nov 2009 15:59:23 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] Installation of igraph on ubuntu 9.10 amd64
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
Hi Lorenzo,
I am trying to install the igraph library on my ubuntu 9.10 system. I
did the procedure which used to work for me in the past
[...]
And no Debian package was produced.
What am I doing wrong? I never had such a problem with signatures
in the past.
The problem is that you don't have my secret key ;) It looks like
dpkg-buildpackage insists on signing the package by default -- I don't
know if that's a recent change or not. Anyway, you can force
dpkg-buildpackage not to sign the package by passing -us -uc in the
command line. Hope this helps.
--
Tamas
------------------------------
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