sonia-users — Discusion list for SoNIA useers

Re: [SoNIA-users] Max pass exceeded etc.

[Skye Bender-d. <sky...@sk...>]

Hi Vivian

On 12/17/2014 02:39 PM, Vivian Ding wrote:
> Hello,
>
> I am trying to use 1_2_2_unstable on networks that are differ quite from
> the ones in social sciences - usually with hundreds of nodes and arcs.Â
> I often get these two types of errors:

Actually, that looks pretty similar to most social science networks :-)


> 1. "KK inner loop exceeded max passes", see the attached screenshot (288
> nodes, 624 arcs, no time dependency). Â  What are the best options to
> avoid it other than reducing the network size?

The screen shot seems to show that optimization process is going fairly 
well, the 'energy' is generally decreasing so the positions are probably 
converging on a "good" layout.  If you want it to try going a little 
longer, you can adjust the "max passes" parameter to something higher 
(perhaps 2000)  to give it a little more time to reach the min epsilon 
energy threshold. Or, if it looks good, you can leave it where it is.

This page gives more explanation of the various parameters for the KK 
layout:

http://sourceforge.net/p/sonia/wiki/Mult-CompKK_layout_parameters/


>
> 2. In similar networks with time-dependency, java program freezes during
> slice playback and has to be restarted.  I have seen it on two separate
> windows 7 machines. Â  Any suggestions?

I'm afraid I don't have enough information to make a suggestion (and I 
don't have a windows 7 machine for testing anymore).  Did it print any 
error messages in the log window?   If you are comfortable starting the 
program from the command line (windows console C: prompt), it may be 
able to print out an error to the console which might give us something 
more to work with.

best,
  -skye

[SoNIA-users] Max pass exceeded etc.

[Vivian D. <viv...@gm...>]

Hello,

I am trying to use 1_2_2_unstable on networks that are differ quite from
the ones in social sciences - usually with hundreds of nodes and arcs.  I
often get these two types of errors:

1. "KK inner loop exceeded max passes", see the attached screenshot (288
nodes, 624 arcs, no time dependency).   What are the best options to avoid
it other than reducing the network size?

2. In similar networks with time-dependency, java program freezes during
slice playback and has to be restarted.  I have seen it on two separate
windows 7 machines.   Any suggestions?


Thanks,


Vivian Ding

[SoNIA-users] Info about SoNIA

[Giulia G. <giu...@sm...>]

Dear Sirs,
I am Giulia Galuzzi and I work for a company, a software house called "Studio Informatica s.r.l" in Italy.
Studio Informatica work on international AML (anti-money laundering)and tax fraud. For example now we are working for the Foreign Account Tax Compliance Act (FATCA).
We work in financial sector and our customers are banks, insurance companies.
We have a different DB and we manage big data and we are trying to develop networks to extract hidden links through SNA.
I start to work with R for multivariate analysis and now I'm interested in Social network analysis.
We are very interested in your project "SONIA" and I wonder if there is opportunity to work with you or get clarification on how to develop a social network.

Regards,
Giulia Galuzzi

Studio Informatica s.r.l.
www.smouse.it<http://www.smouse.it>
Stradone Farnese 43/A 29121 Piacenza
giu...@sm...<mailto:giu...@sm...>
tel: 0523313000
mobile: 3423791484

[SoNIA-users] Import from UCINET?

[frank c. <fra...@ya...>]

Hi all,

I'm new to SoNIA and wanted to upload some UCINET files. I exported a matrix to DL (txt), but when trying to upload this file in SoNIA it says it has not the right extension (.dl). Can anybody give me advice on importing the files in the right way?

Many thanks!

Frank

[SoNIA-users] problem saving movies

[jeffrey l. <jef...@gm...>]

To whom it may concern,

I am a student at Chicago Medical School working on a summer research
project and was interested in using SoNIA to make an animation of a
time-evolving network.  The computer I am working on is running
Windows XP.  I have installed sonia 1.2.2 which I understand is
unstable.  In addition, I recently updated quicktime
version 7 and Java7.  After generating a sequence of graphs as per the
tutorial lab, I tried to save it using "export network --> export
quicktime movie."  This did not generate a file, any fragmented files,
any hidden files, or an error message.  Your help would be greatly
appreciated.

Best Regards,
Jeffrey

Re: [SoNIA-users] Broken install link

[Curtis H. <cur...@gm...>]

Hi Skye,

I'm using the same instructions, but still cannot get the to the  JPEG
Movie Animator in step 3, copied below.

Download the JavaGraphics JPEGMovieAnimation quicktime library from
http://javagraphics.dev.java.net/jars/JPEGMovieAnimation-bin.jar and place
in the lib directory.


On Mon, Jan 7, 2013 at 9:22 AM, Curtis Hampton <cur...@gm...>wrote:

> Hi SoNIA friends,
>
> I'm trying to manually install SoNIA and it appears as if links within
> steps 3 and 4 are broken. Any help installing the program would be much
> appreciated.
>
> Thanks!

Re: [SoNIA-users] Broken install link

[Skye Bender-d. <sky...@sk...>]

Hi Curtis,
  Which instructions are you working from?  The links at 
http://sourceforge.net/apps/mediawiki/sonia/index.php?title=Installing_SoNIA#Installing_SoNIA_Manually

seem to be still working for me.

best,
  -skye

On 01/07/2013 06:22 AM, Curtis Hampton wrote:
> Hi SoNIA friends,
>
> I'm trying to manually install SoNIA and it appears as if links within steps 3 and 4 are broken. Any help installing the program would be much appreciated.
>
> Thanks!
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[SoNIA-users] Broken install link

[Curtis H. <cur...@gm...>]

Hi SoNIA friends, 

I'm trying to manually install SoNIA and it appears as if links within steps 3 and 4 are broken. Any help installing the program would be much appreciated. 

Thanks!

[SoNIA-users] Problem in getting SoNIA started on my data

[Jia Lu <lu...@ya...>]

Dear all,
I just started using SoNIA and having problems after importing my data. I have three waves of data in pajek .net format and the data imported fine into SoNIA. But when I try to follow the steps of creating layout, my data wouldn't even show in the layout window and there are no changes in the schedule window about algorithm convergence. I wonder if it is something wrong with  my data format or any other steps I missed? 

Will someone please help me getting this started? 

Thanks so much!!

Jia 

Re: [SoNIA-users] Ghost / fading links

[Saket N. <sa...@gm...>]

Hi,

Hmm I tried the "Export JPEG Animation (Uncompressed)" option, but it
doesn't seem to be working: I only have 10 slices with 30 nodes, and
it's been 10 minutes and it still says "preparing to start...".  When
I export to Flash it exports immediately.

I got the " Bad version number in .class file" error from the Sonia
installer jar file. I have OS X 10.5.8 with java version 1.5.

Please let me know. Thanks.
Saket


On Tue, Jul 3, 2012 at 2:59 PM, Skye Bender-deMoll <sky...@sk...> wrote:
> Hi Saket,
>
>
> On 07/02/2012 05:40 PM, Saket Navlakha wrote:
>>
>> Thanks. I got the fade-links working under version 1_2_2, but the
>> movie is only smooth and clean for rather small networks (50-100
>> nodes).I have a network with 1000 nodes, and the exported video seems
>>
>> to flash back and forth from previous to future states of the network.
>> I don't get memory errors, so I'm wondering if I'm hitting a known
>> limitation of Sonia? I've only tried exporting to Flash; would
>> Quicktime be better?
>
>
> Yes, the flash movie has a limit on the maximum number objects it will
> export so for long movies (or movies with lots of objects) it will go
> haywire.
>
> The quicktime export is working less and less, as Apple has discontinued
> support for the java libraries.  Think it only works on Windows.   Best
> option is "Export JPEG Animation (Uncompressed)" and then compress the movie
> with an external tool like Handbrake.
>
>
>>
>> Btw, I tried the newest version of Sonia (1_2_2), and it installed
>> fine under Linux for but Mac I get the following error:  "Exception in
>> thread "main" java.lang.UnsupportedClassVersionError: Bad version
>> number in .class file"  -- Please let me know if there's a fix for
>> this.
>
>
> You got this error from the installer, or from SoNIA?  What version of mac
> OS, and java are you using?
>
> best,
>  -skye

Re: [SoNIA-users] Ghost / fading links

[Skye Bender-d. <sky...@sk...>]

Hi Saket,

On 07/02/2012 05:40 PM, Saket Navlakha wrote:
> Thanks. I got the fade-links working under version 1_2_2, but the
> movie is only smooth and clean for rather small networks (50-100
> nodes).I have a network with 1000 nodes, and the exported video seems
> to flash back and forth from previous to future states of the network.
> I don't get memory errors, so I'm wondering if I'm hitting a known
> limitation of Sonia? I've only tried exporting to Flash; would
> Quicktime be better?

Yes, the flash movie has a limit on the maximum number objects it will 
export so for long movies (or movies with lots of objects) it will go 
haywire.

The quicktime export is working less and less, as Apple has discontinued 
support for the java libraries.  Think it only works on Windows.   Best 
option is "Export JPEG Animation (Uncompressed)" and then compress the 
movie with an external tool like Handbrake.

>
> Btw, I tried the newest version of Sonia (1_2_2), and it installed
> fine under Linux for but Mac I get the following error:  "Exception in
> thread "main" java.lang.UnsupportedClassVersionError: Bad version
> number in .class file"  -- Please let me know if there's a fix for
> this.

You got this error from the installer, or from SoNIA?  What version of 
mac OS, and java are you using?

best,
  -skye

Re: [SoNIA-users] Ghost / fading links

[Saket N. <sa...@gm...>]

Thanks. I got the fade-links working under version 1_2_2, but the
movie is only smooth and clean for rather small networks (50-100
nodes). I have a network with 1000 nodes, and the exported video seems
to flash back and forth from previous to future states of the network.
I don't get memory errors, so I'm wondering if I'm hitting a known
limitation of Sonia? I've only tried exporting to Flash; would
Quicktime be better?

Btw, I tried the newest version of Sonia (1_2_2), and it installed
fine under Linux for but Mac I get the following error:  "Exception in
thread "main" java.lang.UnsupportedClassVersionError: Bad version
number in .class file"  -- Please let me know if there's a fix for
this.

Thanks for your help and work.

Saket




On Mon, Jul 2, 2012 at 12:34 PM, Skye Bender-deMoll
<sky...@sk...> wrote:
> Hi Saket,
>  It looks like the "Ghost previous slice" feature is broken.  However I
> think it also doesn't do what you are looking for.  "Ghost previous" is
> supposed to display a grayed-out version of the entire previous network
> image for comparison to the current image.
>
> If you want the links to fade out gradually, I think you want the "Fade old
> events for" option. I just tested that, and it seems to work fine. (I had
> slice delta and duration of one, and set "fad old events for" to 1).  Let me
> know if that works for you.
>
> best,
>  -skye
>
>
> On 06/26/2012 07:26 AM, Saket Navlakha wrote:
>>
>> Hi,
>>
>> I'm trying to use the "ghost previous slice" feature to fade links in
>> and out through time, but for some reason it's not working: I don't
>> see any fading, and instead the links just immediately appear or
>> disappear.
>>
>> I attached the sample file I'm using. Can somebody suggest what may be
>> wrong?
>>
>> Thanks,
>> Saket
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>>
>>
>> _______________________________________________
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Re: [SoNIA-users] Ghost / fading links

[Skye Bender-d. <sky...@sk...>]

Hi Saket,
  It looks like the "Ghost previous slice" feature is broken.  However I 
think it also doesn't do what you are looking for.  "Ghost previous" is 
supposed to display a grayed-out version of the entire previous network 
image for comparison to the current image.

If you want the links to fade out gradually, I think you want the "Fade 
old events for" option. I just tested that, and it seems to work fine. 
(I had slice delta and duration of one, and set "fad old events for" to 
1).  Let me know if that works for you.

best,
  -skye

On 06/26/2012 07:26 AM, Saket Navlakha wrote:
> Hi,
>
> I'm trying to use the "ghost previous slice" feature to fade links in
> and out through time, but for some reason it's not working: I don't
> see any fading, and instead the links just immediately appear or
> disappear.
>
> I attached the sample file I'm using. Can somebody suggest what may be wrong?
>
> Thanks,
> Saket
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> SoNIA-users mailing list
> SoN...@li...
> https://lists.sourceforge.net/lists/listinfo/sonia-users

[SoNIA-users] Ghost / fading links

[Saket N. <sa...@gm...>]

Hi,

I'm trying to use the "ghost previous slice" feature to fade links in
and out through time, but for some reason it's not working: I don't
see any fading, and instead the links just immediately appear or
disappear.

I attached the sample file I'm using. Can somebody suggest what may be wrong?

Thanks,
Saket

[SoNIA-users] horizontal timline layout ?

[Laura R. M. <lau...@ma...>]

Hello,

I am a doctoral student in musicology at McGill University. I've been collecting data regarding the acquisition of a particular technique among string instrument players over the last 50 years, and I'm currently looking for an appropriate network visualization program to map my data.  My data set is relatively small (approx. 100 nodes).
Would you tell me if SoNIA can do the following:

--  Layout of nodes in chronological order.  i.e. I would like the horizontal axis to function as a timeline. Therefore, the x coordinate of each node would be determined by the year in which that musician acquired the technique.
--  vertical clustering of nodes according to a given attribute. The musicians in my study come from 5 different countries, so I'd like the nodes representing each nationality to cluster together. This would have to be vertically, since the horizontal axis is the timeline.

Thanks for your help!

Laura

--

Laura Risk
lau...@ma...
PhD student, musicology
McGill University
www.laurarisk.com

[SoNIA-users] new version of sonia: 1.2.2

[Skye Bender-d. <sky...@sk...>]

After only three years of neglect:

http://sourceforge.net/projects/sonia/files/sonia/sonia_1_2_2_unstable/


Its labeled "unstable" because there still known bugs, but at least the
installer should be working now, and some other major issues fixed.
The readme has more information about some new features, and a helper
program. Please let me know if the installer works for you!

best,
 -skye

Re: [SoNIA-users] sonia 1.2.1

[Skye Bender-d. <sky...@sk...>]

I've been trying to get around to a release for the past year or so. The
source code version uses a non-apple quicktime library to do the qt
movie export, so still works.  But it also contains other bugs and
uncompleted features.  Should I just release it, warts and all?  Thoughts?



On 10/15/10 10:46 AM, Simone Gabbriellini wrote:
> Hello,
> 
> is there a prevision for the release of 1.2.1? I've seen that since quicktime X has been released, QTJava are considered deprecated by Apple and I cannot accomplish much with the swf exporter, I always run out of memory, even if I use
> 
> java -cp sonia_1_2_0.jar sonia.SoniaController -Xms516M -Xmx1024M
> 
> thanks,
> simone
> 
> 
> 
> 
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[SoNIA-users] sonia 1.2.1

[Simone G. <sim...@gm...>]

Hello,

is there a prevision for the release of 1.2.1? I've seen that since quicktime X has been released, QTJava are considered deprecated by Apple and I cannot accomplish much with the swf exporter, I always run out of memory, even if I use

java -cp sonia_1_2_0.jar sonia.SoniaController -Xms516M -Xmx1024M

thanks,
simone

[SoNIA-users] export qt movies

[Simone G. <sim...@gm...>]

Hello List,

I have manually installed SoNIA and everything runs fine. The only step I am missing is the QTJava.zip, which appears not to be on my system.

I've searched on my computer for the zip file, but I haven't found it. I have already installed Quicktime X on my Mac OSX 10.6. Maybe with this release of quicktime there's a different way to connect to the QTjava?

any help more than welcome,
best regards,
Simone Gabbriellini

Panmind Labs,
Polo Universitario di Siena
Colle di Val d'Elsa.

http://panmind.org
http://www.digitaldust.it

Re: [SoNIA-users] Deal with isolates

[Skye Bender-d. <sky...@sk...>]

SoNIA does not currently have any built in methods for removing or
hiding isolates.   You could pre-process you networks to hide isolates.
 However, if you already have duration information for the nodes,
perhaps the fact that there are isolates reflects real properties of the
network?

There are a few brute-force options for specifying isolate positions
(pin to circle, pin to bottom, etc). Since an isolate is also a
component, you can also use the distance between components property in
the KK algorithm to have the isolates positioned as well, tho this may
introduce some other distortion in the layout.

best,
 -skye

On 9/5/10 7:48 AM, Marcus Drescher wrote:
> Dear Sonia members,
> 
> I want to visualize a network over 50 periods. During that time I have a lot of vertices appearing and disappearing. At total over all periods there are 106 distinct vertices.
> 
> When I want to visualize the network there are at least 50 isolates at the same time. Is there a way to remove them from the "graph"?
> 
> Or, maybe, is it due to the use of rSoNIA and the dynamicnetwork package that I have to keep the isolates over time in the sample?
> 
> I am glad for all advice.
> Thanks in advance.
> 
> Marcus
> 
> 
> 
> 
> 
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[SoNIA-users] Deal with isolates

[Marcus D. <dre...@tu...>]

Dear Sonia members,

I want to visualize a network over 50 periods. During that time I have a lot of vertices appearing and disappearing. At total over all periods there are 106 distinct vertices.

When I want to visualize the network there are at least 50 isolates at the same time. Is there a way to remove them from the "graph"?

Or, maybe, is it due to the use of rSoNIA and the dynamicnetwork package that I have to keep the isolates over time in the sample?

I am glad for all advice.
Thanks in advance.

Marcus

Re: [SoNIA-users] a problem with the installation of SoNIA.

[Skye Bender-d. <sky...@sk...>]

The wiki page is probably a good starting point

http://sourceforge.net/apps/mediawiki/sonia/

On 8/27/10 5:21 PM, Bo Liang wrote:
> 
> Hi all,
> 
> I'm new to SoNIA and just installed it in my computer. I don't know how to use it. Where can I find some documents about how to collect data and write the original data file? 
> 
> Thanks.
> Xinxin 		 	   		  
> 
> 
> 
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Re: [SoNIA-users] a problem with the installation of SoNIA.

[Bo L. <lia...@ho...>]

Hi all,

I'm new to SoNIA and just installed it in my computer. I don't know how to use it. Where can I find some documents about how to collect data and write the original data file? 

Thanks.
Xinxin 		 	   		  

Re: [SoNIA-users] size limits

[Skye Bender-d. <sky...@sk...>]

Emily Erikson wrote:
> Hi,
> I'm trying to use Sonia to visualize a largish firm-collaboration 
> network, 14,507 nodes and 138,739 arc events.

Thats at least an order of magnitude larger than anything I've ever
worked with successfully ;-)

> It doesn't seem that much larger than the Christakis Fowler obestity 
> network -- but I'm not having much luck. Lots of CPU use, no 
> visualization -- although no error message either.

I'm pretty sure they only visualized the largest connected component.

> 
> Is this the kind of thing that if I give it enough time it will work? or 
> maybe it should work and there is something I'm not doing correctly. any 
> help would be great.

I imagine it will churn for a very long time and eventually run out of
memory.  Probably need to figure out a relevant subset of nodes to
visualize instead.

best,
 -skye

[SoNIA-users] size limits

[Emily E. <er...@so...>]

Hi,
I'm trying to use Sonia to visualize a largish firm-collaboration 
network, 14,507 nodes and 138,739 arc events.
It doesn't seem that much larger than the Christakis Fowler obestity 
network -- but I'm not having much luck. Lots of CPU use, no 
visualization -- although no error message either.

Is this the kind of thing that if I give it enough time it will work? or 
maybe it should work and there is something I'm not doing correctly. any 
help would be great.

Emily