Re: [igraph] igraph-help Digest, Vol 83, Issue 6

[Abby Rudolph]

Thank you Tam and Gabor for your help with qaptest.  I was able to convert it 
to an adjacency matrix using get.adjacency(), however, it drops  the alter tie 
descriptors, which I need for the quadratic assignment procedure.  The result 
is a 3020*3020 matrix of class "dgCMatrix".  In my original dataset, I had 3020 
individuals,  but I also had 26 tie attributes which I was going to use for the 
qap hypothesis testing procedure.  Do you know what format the procedure needs 
the data to be in in order to test the correlation between two types of alter 
connections with qap?

Thanks,
Abby

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Today's Topics:

   1. Re: plot.bgraph (Tam?s Nepusz)
   2. Union of two directed graphs in R (Matt Rissler)
   3. Re: Union of two directed graphs in R (Matt Rissler)
   4. Re: Union of two directed graphs in R (Tam?s Nepusz)
   5. Re: using  qaptest (Tam?s Nepusz)
   6. Re: using qaptest (G?bor Cs?rdi)
   7. Re: plot.bgraph (G?bor Cs?rdi)


----------------------------------------------------------------------

Message: 1
Date: Fri, 7 Jun 2013 20:42:42 +0200
From: Tam?s Nepusz <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] plot.bgraph
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii

> I'm trying to use the implementation of cohesive.blocks in igraph_0.6.5-2 on 
> R 3.0.1. It appears to return the block structure, more or less as expected. 
> The problem I'm running into is then trying to use the corresponding 
> plot.bgraph to plot the block structure. I get:
> Error: could not find function "plot.bgraph"
> Has this feature been dropped?
Not sure -- Gabor can tell you more, but I think that it is gone because igraph 
0.6 can plot overlapping groups now, so you can simply call plot() with your 
block structure as the first and the graph as the second argument, and igraph 
will plot the graph and highlight the groups for you. This is not the same plot 
as plot.bgraph used to produce but maybe it's easier to digest.

--
Tamas


------------------------------

Message: 2
Date: Fri, 7 Jun 2013 14:23:03 -0500
From: Matt Rissler <address@hidden>
To: address@hidden
Subject: [igraph] Union of two directed graphs in R
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"

I'm trying to union two directed graphs by name and I get the following
error.

graph.union.by.name(AAD,ACC)

Error: !is.directed(g1) & !is.directed(g2) is not TRUE

The documentation intimates that this should work.  Does the check need to
be changed to a not xor.

Thanks,

Matt

-- 
Matt Rissler
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Message: 3
Date: Fri, 7 Jun 2013 14:27:40 -0500
From: Matt Rissler <address@hidden>
To: address@hidden
Subject: Re: [igraph] Union of two directed graphs in R
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"

But looking at the source, the comment distinctly states that that directed
are not allowed?  Does this work in Python?  If so, back to SAGE for this
project.

Thanks again.


On Fri, Jun 7, 2013 at 2:23 PM, Matt Rissler <address@hidden> wrote:

> I'm trying to union two directed graphs by name and I get the following
> error.
>
> graph.union.by.name(AAD,ACC)
>
> Error: !is.directed(g1) & !is.directed(g2) is not TRUE
>
> The documentation intimates that this should work.  Does the check need to
> be changed to a not xor.
>
> Thanks,
>
> Matt
>
> --
> Matt Rissler
>
>


-- 
Matt Rissler
2350 Pearl St
Dubuque, IA 52001
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Message: 4
Date: Fri, 7 Jun 2013 22:05:55 +0200
From: Tam?s Nepusz <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] Union of two directed graphs in R
Message-ID: <address@hidden>
Content-Type: text/plain; charset=iso-8859-1

> But looking at the source, the comment distinctly states that that directed 
> are not allowed?  Does this work in Python?  If so, back to SAGE for this 
> project.
I cannot comment on the R part of this question but I can say that the Python 
interface has no implementation yet for graph_union_by_name (or any of the 
other _by_name methods).

-- 
T.




------------------------------

Message: 5
Date: Fri, 7 Jun 2013 22:09:25 +0200
From: Tam?s Nepusz <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] using  qaptest
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii

> In what format does the data need to be in order to run the quadratic 
> assignment procedure in R?
Since qaptest is part of the sna package, I strongly suspect that you need to 
convert your igraph graph into sna's network format. There is an R package 
named "intergraph" that you could probably use -- as far as I know, it allows 
you to convert between several R network formats.

-- 
T.


------------------------------

Message: 6
Date: Fri, 7 Jun 2013 21:47:51 -0400
From: G?bor Cs?rdi <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] using qaptest
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"

sna uses adjacency matrices AFAIK, so you can just convert with
get.adjacency().


Gabor


On Fri, Jun 7, 2013 at 4:09 PM, Tam?s Nepusz <address@hidden> wrote:

> > In what format does the data need to be in order to run the quadratic
> assignment procedure in R?
> Since qaptest is part of the sna package, I strongly suspect that you need
> to convert your igraph graph into sna's network format. There is an R
> package named "intergraph" that you could probably use -- as far as I know,
> it allows you to convert between several R network formats.
>
> --
> T.
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
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Message: 7
Date: Sat, 8 Jun 2013 11:22:44 -0400
From: G?bor Cs?rdi <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] plot.bgraph
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"

Yep, plot.graph is gone, in favor of the new kind of plotting and
plotHierarchy(). Look at the cohesive.blocks manual page.

G.


On Fri, Jun 7, 2013 at 2:42 PM, Tam?s Nepusz <address@hidden> wrote:

> > I'm trying to use the implementation of cohesive.blocks in
> igraph_0.6.5-2 on R 3.0.1. It appears to return the block structure, more
> or less as expected. The problem I'm running into is then trying to use the
> corresponding plot.bgraph to plot the block structure. I get:
> > Error: could not find function "plot.bgraph"
> > Has this feature been dropped?
> Not sure -- Gabor can tell you more, but I think that it is gone because
> igraph 0.6 can plot overlapping groups now, so you can simply call plot()
> with your block structure as the first and the graph as the second
> argument, and igraph will plot the graph and highlight the groups for you.
> This is not the same plot as plot.bgraph used to produce but maybe it's
> easier to digest.
>
> --
> Tamas
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
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