Skip to main content
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] [List Home]
Re: [stem-dev] VIRUSVESZELY!!! - Pajek graph- specifying dates and rates

Hi Tekla,


I have managed to make the pajek graph work with a network of around 68,000 nodes using the LibreOffice template. How many nodes were you trying to use?


Have you ever tried specifying more dates and rates for the edges? As on the web page?


1 2 popID beef rate 1.0 date 2012-01-01 rate 10.0

If so, have you ever had success with this?


Hopefully both of our problems will be able to be resolved.


Looking forward to talking to you on the STEM call on Thursday. 


Best wishes,


Emily



Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389
From: Engelhardt Tekla <EngelhardtT@xxxxxxxxxxxx>
Sent: 25 September 2018 11:46:04
To: developer mailing list STEM; Emily Nixon
Subject: Re: VIRUSVESZELY!!! - [stem-dev] Pajek graph- specifying dates and rates
 
Dear All, 
We also had some problem with the Pajek graph, especially when we made with LibreOffice template, it did not work, so we made the Pajek graph with Knime. We used the form found on the website (https://wiki.eclipse.org/Importing_a_Pajek_Graph):
*Vertices 3
1 Berlin 1 1 popID men popCount 100 popID women popCount 110
2 Bonn 1.5 1 popID men popCount 100 popID women popCount 110
3 Germany 1.2 1.2
*Edges
1 2 popID men rate 0.1
2 1 popID women rate 0.2
3 1 
In that way it’s seemed to be work, but we think not a proper way. We noticed some movements, but it wasn’t as much as it could be. We noticed some disease spread between nodes, but based on data and parameters it should be more and more. We tried a small Pajek file firstly and it was OK, but when we tried with much more larger network it “failed”.
And for last but not least we also would like to connect to each other the Pajek file ( pig movements) and the shape file (wild boar population density), but yet it is not solved. So we also noticed some errors with a Pajek, what is noticed by Emily and we also have a question according to Pajek and shape files. 
We also will be on the STEM phone call on Thursday. 

Best wishes, 

Tekla


Dr. Engelhardt Tekla
elemző

Nemzeti Élelmiszerlánc-biztonsági Hivatal
Rendszerszervezési és Felügyeleti Igazgatóság
Tervezési Osztály

1024 Budapest, Kis Rókus utca 15/B.
06-70/508-1834
EngelhardtT@xxxxxxxxxxxx
portal.nebih.gov.hu

Tekla ENGELHARDT, PhD
analyst

National Food Chain Safety Office
System Management and Supervision Directorate

H-1024 Budapest, Kis Rókus utca 15/B.
+36-70/508-1834
EngelhardtT@xxxxxxxxxxxx

On 2018. September 21. at 17:33:21, Nixon Emily (emily.nixon@xxxxxxxxxxxxx) wrote:

Hi all,


I'm now in the final year of my PhD and realised that I urgently need to make a change in my model by using a feature in the pajek graphs that I haven't before. 


My pajek graphs so far have never included the optional parameters specified on the wiki:


Optional parameters:

  • date - specification a of date at which the migration rate is different from the standard value specified in the obligatory parameters. ISO 8601 standard is used (YYYY-MM-DD). This parameter may be used repeatedly.
  • rate - migration rate for the specified date. This parameter may be used repeatedly. The associated date is the last mentioned one.

https://wiki.eclipse.org/Importing_a_Pajek_Graph


I've made a dummy pajek graph to test using these optional parameters. However, even though I've specified them, they don't seem to be implemented. 


I first noticed this in my Marketdummy1 scenario, where I specified much higher rates than the baseline rate on particular dates (this is what I'm planning on doing in my model). I would expect that on the specified dates, more sheep would move between certain nodes than on a normal date, but this didn't seem to be happening. 


In Marketdummy2A, I've tried specifying really high rates (e.g. 1 which I think is the maximum), just on the specified days and then have no baseline rate. If it was working, then I would expect there to only be movements on the specified dates. However, there are no movements between nodes at all. 


In case the value "1" was too high to use multiple times, I made the baseline zero again and then this time had a rate of 0.2 on the specified dates (I haven't attached this model, but I've attached the spreadsheet Marketdummy3). There were still no movements between nodes. 


I also tried selecting the options "use global Region Names" and "Move Nodes to Containers" when importing the pajek graph into STEM, just in case this was why the specified dates and rates were not taken into account. Again, no luck.


If anyone can help, then please let me know! I think this might be a bug, but I thought I would check with you before opening one. I have attached the project I was using and the spreadsheet I used to make the pajek graph. This is the spreadsheet that can be downloaded from the wiki and used to produce a net file in Libre Office). I have also attached the net files produced.  https://wiki.eclipse.org/Importing_a_Pajek_Graph 


Best wishes,


Emily 




Emily Nixon
PhD Student

Demonstrator
School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389
_______________________________________________
stem-dev mailing list
stem-dev@xxxxxxxxxxx
To change your delivery options, retrieve your password, or unsubscribe from this list, visit
https://dev.eclipse.org/mailman/listinfo/stem-dev

Back to the top