Re: [stem-dev] VIRUSVESZELY!!! - Pajek graph- specifying dates and rates

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Re: [stem-dev] VIRUSVESZELY!!! - Pajek graph- specifying dates and rates

From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
Date: Wed, 26 Sep 2018 11:50:57 +0000
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Thread-topic: VIRUSVESZELY!!! - [stem-dev] Pajek graph- specifying dates and rates

Hi Tekla,

I have a lot of edges too, but they work using the baseline migration rate. It's just the dates and rates which don't seem to have an impact on the results (e.g. in the examples I sent in my first email).

So I think that the dates and rates part of the pajek perhaps aren't being registered somehow when read into STEM. They don't show up in the STEM GUI and when you right-click to display the graph, there are no edge labels (which I assume is what dates and rates are?), but node labels seem to have been added from the pajek graph and can also be added manually. In the source code (org.eclipse.stem.core.impl) it seems that there are supposed to be edge labels.

When I read my pajek graph with dates and rates into stem, as it is still generally functional, I only recently realised that I sometimes still get an error log (attached) with message "The object 'org.eclipse.stem.definitions.edges.impl.MigrationEdgeLabelValueImpl@17aee70e (migrationRate: 0.01, timePeriod: 86400000)' is not contained in a resource."

This might explain more what is going on. Do you also get an error log? Does anyone else know what this might mean? I've been trying to look at the source code that is referenced, but haven't worked it out yet.

If anyone who thinks they might be able to help us has a chance to look at this before the teleconference then that would be great. I am sure we will have good discussions about this tomorrow.

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: 26 September 2018 08:13:09
To: Emily Nixon
Subject: Re: VIRUSVESZELY!!! - [stem-dev] Pajek graph- specifying dates and rates

Hi,

We have less nodes (20.000-30.000), but huge number of edges, we tried specifying dates and rates but we do not sure it succeed. We detect some spread but we think it should be more… At one point we postpone this question and problem and we started the work with shape file, but soon we have to continue with the Pajek…

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

http://www.facebook.com/nebih.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 25. at 13:56:20, Nixon Emily (emily.nixon@xxxxxxxxxxxxx) wrote:

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
http://www.facebook.com/nebih.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

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eclipse.buildId=unknown
java.version=1.8.0_181
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=en_GB
Command-line arguments:  -os win32 -ws win32 -arch x86_64 -console -consoleLog

org.eclipse.stem.definitions
Error
Wed Sep 26 12:09:44 BST 2018
The object 'org.eclipse.stem.definitions.edges.impl.MigrationEdgeLabelValueImpl@17aee70e (migrationRate: 0.01, timePeriod: 86400000)' is not contained in a resource.

org.eclipse.emf.ecore.resource.Resource$IOWrappedException: The object 'org.eclipse.stem.definitions.edges.impl.MigrationEdgeLabelValueImpl@17aee70e (migrationRate: 0.01, timePeriod: 86400000)' is not contained in a resource.
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.endSave(XMLSaveImpl.java:301)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.save(XMLSaveImpl.java:265)
	at org.eclipse.emf.ecore.xmi.impl.XMLResourceImpl.doSave(XMLResourceImpl.java:389)
	at org.eclipse.emf.ecore.resource.impl.ResourceImpl.save(ResourceImpl.java:1430)
	at org.eclipse.emf.ecore.resource.impl.ResourceImpl.save(ResourceImpl.java:999)
	at org.eclipse.stem.core.Utility.serializeIdentifiables(Utility.java:399)
	at org.eclipse.stem.core.Utility.serializeIdentifiable(Utility.java:335)
	at org.eclipse.stem.graphgenerators.impl.PajekNetGraphGeneratorImpl.getGraph(PajekNetGraphGeneratorImpl.java:622)
	at org.eclipse.stem.graphgenerators.impl.PajekNetGraphGeneratorImpl.getGraph(PajekNetGraphGeneratorImpl.java:515)
	at org.eclipse.stem.ui.graphgenerators.adapters.graphgeneratorpropertyeditor.GraphGeneratorPropertyEditor.getGraph(GraphGeneratorPropertyEditor.java:314)
	at org.eclipse.stem.ui.graphgenerators.wizards.GraphGeneratorPropertyComposite.getGraph(GraphGeneratorPropertyComposite.java:127)
	at org.eclipse.stem.ui.graphgenerators.wizards.GraphGeneratorDefinitionControl.getGraph(GraphGeneratorDefinitionControl.java:235)
	at org.eclipse.stem.ui.graphgenerators.wizards.NewGraphWizard$NewGraphPage.getGraph(NewGraphWizard.java:189)
	at org.eclipse.stem.ui.graphgenerators.wizards.NewGraphWizard.createIdentifiable(NewGraphWizard.java:122)
	at org.eclipse.stem.ui.wizards.NewIdentifiableWizard.createIdentifiable(NewIdentifiableWizard.java:238)
	at org.eclipse.stem.ui.wizards.NewIdentifiableWizard$1.execute(NewIdentifiableWizard.java:181)
	at org.eclipse.ui.actions.WorkspaceModifyOperation$1.run(WorkspaceModifyOperation.java:106)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2313)
	at org.eclipse.ui.actions.WorkspaceModifyOperation.run(WorkspaceModifyOperation.java:118)
	at org.eclipse.jface.operation.ModalContext.runInCurrentThread(ModalContext.java:466)
	at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:374)
	at org.eclipse.jface.wizard.WizardDialog.run(WizardDialog.java:1059)
	at org.eclipse.stem.ui.wizards.NewIdentifiableWizard.performFinish(NewIdentifiableWizard.java:191)
	at org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDialog.java:853)
	at org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDialog.java:438)
	at org.eclipse.stem.ui.wizards.STEMWizardDialog.buttonPressed(STEMWizardDialog.java:36)
	at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:619)
	at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:248)
	at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
	at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4353)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1061)
	at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4172)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3761)
	at org.eclipse.jface.window.Window.runEventLoop(Window.java:832)
	at org.eclipse.jface.window.Window.open(Window.java:808)
	at org.eclipse.stem.ui.graphgenerators.wizards.NewGraphWizard$NewGraphWizardCommandHandler.execute(NewGraphWizard.java:214)
	at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:294)
	at org.eclipse.ui.internal.handlers.E4HandlerProxy.execute(E4HandlerProxy.java:90)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
	at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:247)
	at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:229)
	at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132)
	at org.eclipse.e4.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:149)
	at org.eclipse.core.commands.Command.executeWithChecks(Command.java:499)
	at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
	at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
	at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:825)
	at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.handleWidgetSelection(HandledContributionItem.java:701)
	at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.access$6(HandledContributionItem.java:685)
	at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem$4.handleEvent(HandledContributionItem.java:613)
	at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
	at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4353)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1061)
	at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4172)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3761)
	at org.eclipse.jface.window.Window.runEventLoop(Window.java:832)
	at org.eclipse.jface.window.Window.open(Window.java:808)
	at org.eclipse.ui.internal.views.log.EventDetailsDialog.open(EventDetailsDialog.java:181)
	at org.eclipse.ui.internal.views.log.EventDetailsDialogAction.run(EventDetailsDialogAction.java:98)
	at org.eclipse.ui.internal.views.log.LogView$15.doubleClick(LogView.java:537)
	at org.eclipse.jface.viewers.StructuredViewer$1.run(StructuredViewer.java:831)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:50)
	at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:178)
	at org.eclipse.jface.viewers.StructuredViewer.fireDoubleClick(StructuredViewer.java:828)
	at org.eclipse.jface.viewers.AbstractTreeViewer.handleDoubleSelect(AbstractTreeViewer.java:1472)
	at org.eclipse.jface.viewers.StructuredViewer$4.widgetDefaultSelected(StructuredViewer.java:1237)
	at org.eclipse.jface.util.OpenStrategy.fireDefaultSelectionEvent(OpenStrategy.java:252)
	at org.eclipse.jface.util.OpenStrategy.access$0(OpenStrategy.java:249)
	at org.eclipse.jface.util.OpenStrategy$1.handleEvent(OpenStrategy.java:311)
	at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
	at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4353)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1061)
	at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4172)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3761)
	at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1151)
	at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
	at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1032)
	at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:148)
	at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:636)
	at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
	at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:579)
	at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
	at org.eclipse.stem.ui.launcher.WorkbenchLauncher.launch(WorkbenchLauncher.java:47)
	at org.eclipse.stem.core.common.presentation.CoreEditorAdvisor$Application.start(CoreEditorAdvisor.java:409)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:648)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:603)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1465)
Caused by: org.eclipse.emf.ecore.xmi.DanglingHREFException: The object 'org.eclipse.stem.definitions.edges.impl.MigrationEdgeLabelValueImpl@17aee70e (migrationRate: 0.01, timePeriod: 86400000)' is not contained in a resource.
	at org.eclipse.emf.ecore.xmi.impl.XMLHelperImpl.handleDanglingHREF(XMLHelperImpl.java:754)
	at org.eclipse.emf.ecore.xmi.impl.XMLHelperImpl.getURIFragment(XMLHelperImpl.java:725)
	at org.eclipse.emf.ecore.xmi.impl.XMLHelperImpl.getIDREF(XMLHelperImpl.java:747)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveIDRefSingle(XMLSaveImpl.java:1992)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1333)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1224)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElementID(XMLSaveImpl.java:2716)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElement(XMLSaveImpl.java:1181)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElement(XMLSaveImpl.java:1042)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveContainedMany(XMLSaveImpl.java:2417)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1553)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1224)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElementID(XMLSaveImpl.java:2716)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElement(XMLSaveImpl.java:1181)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElement(XMLSaveImpl.java:1042)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveContainedMany(XMLSaveImpl.java:2417)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1553)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveFeatures(XMLSaveImpl.java:1224)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.saveElementID(XMLSaveImpl.java:2716)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.writeTopObject(XMLSaveImpl.java:683)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.traverse(XMLSaveImpl.java:591)
	at org.eclipse.emf.ecore.xmi.impl.XMLSaveImpl.save(XMLSaveImpl.java:251)
	... 99 more

References:
- [stem-dev] Pajek graph- specifying dates and rates
  - From: Emily Nixon
- Re: [stem-dev] VIRUSVESZELY!!! - Pajek graph- specifying dates and rates
  - From: Engelhardt Tekla
- Re: [stem-dev] VIRUSVESZELY!!! - Pajek graph- specifying dates and rates
  - From: Emily Nixon

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