Introduction to Exploratory Network Analysis for Archaeologists using visone

55 Pages·2015·8.79 MB·English

Introduction to Exploratory Network Analysis
for Archaeologists using visone
Daniel Weidele, Tom Brughmans
This version
July 5, 2017
Contents
Exercise-1: InstallingandStartingVisone. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1 Introduction 4
1.1 Welcometovisone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 TutorialOverview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 visoneInterface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3.1 MenuBar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.2 ToolBar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.3.3 InteractionModes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.4 Reminders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Exercise0: DrawingaNewNetwork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2 CSV-basedFileFormats 17
2.1 AdjacencyMatrix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2 AdjacencyList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3 EdgeList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.4 OtherFileFormats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Exercise1: LoadingtheDataSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3 NetworkEditing 22
3.1 VisoneAttributeManager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Exercise2: ImportingadditionalSiteAttributes . . . . . . . . . . . . . . . . . . . . . . . . . 25
Exercise3: FilteringandDeletingNodes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Exercise4: ConfiguringandManipulatingLinkAttributes . . . . . . . . . . . . . . . . . . . . 30
Exercise5: TransformingLinks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4 NetworkAnalysis 34
4.1 Centralities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Exercise6: ComputationofBetweennessandCloseness . . . . . . . . . . . . . . . . . . . . . 35
4.2 Clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Exercise7: Girvan-NewmanClustering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5 NetworkVisualization 39
5.1 MappingtoVisualVariables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Exercise8: MappingtoVisualVariables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
5.2 NodePositioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Exercise9: MapLayoutandOverlapRemoval. . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Exercise10: StressMinimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
6 Export 49
7 Discussion 50
8 OtherSoftwareResources 51
9 FurtherReading 52
2
Exercise -1: Installing visone
Thegoalofthisexerciseistohavevisonerunningonyourcomputer.
Fordetailedinstallationinstructionspleasecheckouttheo�cialvisoneWikihere:
http://visone.info/wiki/index.php/Installation_%28trail%29
Requirement:
JavaSEisinstalledonyouroperatingsystem:
2 http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
Varianta)Webstart:
Visithttp://visone.info/withyourwebbrowser.
2 ClickWebstarttolaunchvisonedirectlyfromthebrowser.
2
Variantb)LocalInstallation:
Downloadthecurrentstablevisoneversionhere:
2 http://visone.info/html/download.html
Run the downloaded v i s o n e JAR file by double-clicking the downloaded file, or executing the fol-
2
java -jar visone-x.x.x.jar
lowing command:
Tip: Youcanrunvisonewithmorememorybyspecifyinge.g. -Xmx2gfor2GBofmemory:
java -Xmx2g -jar visone-x.x.x.jar
Result
Youseethegraphicaluserinterfaceofvisone.
2
Figure1:Graphicaluserinterfaceofvisoneafterstartup.
Youaccomplishedtheexercise:-)
Nowyouarereadyforthetutorial!
3
Chapter 1
Introduction
1.1 Welcome to visone
So,youfinallydecidedtogetintothebasicsofvisone. That’sgreat! visoneisdevelopedbythemembers
oftheAlgoritmicsGroupoftheDepartmentofComputerandInformationScienceattheUniversityof
Konstanz. Itisafreeresearchtoolanddoesnotaimforanykindofcommercialization. visoneallows
youtoapplyvariousalgorithmsandmethodsinordertoanalyzeandvisualizenetworks. Thistutorial
ismeantforbeginnerswhohavelittleornoexperiencewithNetworkScience.
Youcanfindmoreadvancedtutorialsandfurtherinformationhere:
http://visone.info/wiki/index.php/Main_Page
Also,incaseyouexperienceanytrouble,theo�cialvisonenewsgroupmightbeofinteresttoyou:
https://groups.google.com/forum/#!forum/visone-users
Thetutorialisbuiltupinthefollowingway:
Wewillfirsthaveagenerallookatthevisonegraphicaluserinterface.
•
ThenextchaptersaddressNetworkSciencetopics,wherewithinachapter
•
– first,weexplainmethodologicalbasics,and
– thenyoucanactivelyexperiencevisonethroughoutexercises.
Thiswayofapproachingthetopicshallemphasizetheimportanceofunderstandingtheprin-
ciplesbehindthemethodso↵eredinvisonebefore applyingthem,tonoteventuallyendup
withmisleadinginterpretationofthedata.
ThelastchapterspointoutmoreNetworkSciencesoftwareresourcesandadvancedreadingmate-
•
rial.
1.2 Tutorial Overview
Throughoutthistutorialyouwillcreate2networkvisualizationsofaMayaobsidiannetwork. Youwill
gettoknowmoredetailsonthedatasetatthebeginningofexercise1. Figure2providesanoverview
aboutthemethodologicalpipelineyouwillrunthroughwithin10exercises.
Thegeneralstepsareasfollows:
LoadingthedatasetfromCSVfiles(Exercise1&2).
2
Filteringandeditingthenetwork(Exercise3to5).
2
Computationofcentralitymeasures(Exercise6).
2
Clusteringofnodes(Exercise7).
2
Visualizations(Exercise8to10).
2
4
5
Figure2:TutorialOverview. Throughout10exercisesyouwilllearnhowtoloadaMayaobsidiannetworkinvisone. Innextstepsyouwillrevealmore
structureofthenetworkbyfilteringnodesandedgesfromthehairball. Centralitymeasuresandclusteringwillprovidefurtherinsightintothe
network. Inthelaststepsyouwillseehowtoproducevisualizationsbymappingattributedatatovisualvariablesandapplyingmeaningful
layouttechniques.
1.3 visone Interface
Figure3showstheinterfaceofvisone.
Figure3:GraphicalUserInterfaceofvisone.
Thereisamenubar atthetopofthewindowcontainingthemenusfile,edit,nodes,links,view
2 andabout.
Belowthemenubaryoufindatoolbar o↵eringquickaccesstogeneralfunctions.
2
Ontherightyoufindthenetworkpanel showingabasicnetworkwith6nodesand7edges.
2
Ontheleftbelowthetoolbarthereisanetworkoverviewpanelwhichprovidesanoverviewabout
2 thenetworkandhighlightstheviewportofthenetworkpanelingrey.
Below the network overview panel you can find a search box to quickly access algorithms and
2 methods.
Belowthesearchboxthereare4tabs eachgroupingmethodsforanalyzing,visualizing,modeling
2 andtransforminganetwork.
Within a tab panel you can select and configure a method, e.g. in figure 3 there is selected a
2 methodtocomputethedegreeofthenetworknodes.
Belowthetabpanelthereisacontrolpanel whereyoucanchooseanetworktoapplyamethod
2 on,getsomeinfoonthemethoditselfandexecuteamethodbyclickingonanalyze.
6
1.3.1 Menu Bar
Themenubarisstructuredin6menus:
Filemenu
new-createanewnetworkinthenetworkpanel
•
open-loadanetworkfromfile
•
create-generateanetworkbywithnetworkgen-
•
erationalgorithms
createcopy-createacopyofthecurrentlydis-
•
playednetworkinthenetworkpanel
save-savethecurrentlydisplayednetwork
•
save as... - open the save dialog to save the
•
currentlydisplayednetworkwithdi↵erentname
orformat
export-exportthecurrentlydisplayednetwork
•
asimage,PDForotherspecialfileformats
print-printoutthecurrentlydisplayednetwork
•
options -changegeneralsettingsof visoneand
•
setupextensions(e.g. connectiontoR)
closenetwork-closethecurrentlydisplayednet-
•
work
exit -exitvisone
• Figure4:Filemenuofthevisonemenubar.
Editmenu
selectall -selectallnodesandedges
•
deselectall-deselectanyselectednodesoredges
•
invertselection-inverttheselectionofselected
•
nodesandedges
cut-cutthecurrentlyselectednodesandedges
•
copy - copy the currently selected nodes and
•
edges
paste-pastethenodesandedgesthathavebeen
•
cutorcopiedbeforeintothecurrentlydisplayed
network Figure5:Editmenuofthevisonemenubar.
7
Nodesmenu
deletenodes-deletethecurrentlyselectednodes
•
delete isolates - delete the nodes that are not
•
connectedtoanyothernode(calledisolates)
deleteallgroupnodes-deleteallnodesthatrep-
•
resentagroupofnodes(calledgroups)
selectall -selectallnodes
•
deselectall -deselectallnodes
•
select neighbors -expandthecurrentselection
•
ofnodesbyadditionallyselectingtheirdirectly
connectednodes(calledneighbors)andedges
selectincidentlinks -expandthecurrentselec-
•
tionofnodesbyadditionallyselectinganydirect
linksbetweentheselectednodes
invertselection-inverttheselectionofselected
•
nodes
• selectgroups-selectallgroupnodes Figure6:Nodesmenuofthevisonemenubar.
templates-opensthenodetemplatedialog
•
properties-opensthenodepropertiesdialog
•
Linksmenu
deletenodes-deletethecurrentlyselectedlinks
•
deleteloops -deletelinksfromanodetoitself
•
(calledloops)
delete bends - delete anchor points of links
•
(calledbends)
reverse direction - reverse the direction of di-
•
rectedlinks
makedirected -makeundirectedlinksdirected
•
make undirected - make directed links undi-
•
rected
selectall -selectalllinks
•
deselectall -deselectalllinks
•
invertselection-inverttheselectionofselected
•
links
templates-opensthelinktemplatedialog
•
properties-opensthelinkpropertiesdialog
• Figure7:Linksmenuofthevisonemenubar.
8
Viewmenu
zoomin-increasethezoomlevelofthenetwork
•
panel
zoomout -decreasethezoomlevelofthenet-
•
workpanel
zoom100% -zoomthenetworkpanelto100%
•
fitnetwork-fitthewholenetworkintothenet-
•
workpanel
fit all networks - fit all opened networks into
•
theirrespectivenetworkpanels
refresh-refreshthenetworkpanel
•
draw multi-links - allow the network panel to
•
displaymorethanonelinkbetweentwonodes
(calledmulti-links)
clearbackground-removethebackgroundofthe
•
networkpanel
modes -changetheinteractionmodewiththe Figure8:Viewmenuofthevisonemenubar.
•
networkpanel(analysis,edit andstressmode).
Aboutmenu
about visone - get some information about
• visone(versionnumber,linktowebsite,licenses)
Figure9:Aboutmenuofthevisonemenubar.
9
1.3.2 Tool Bar
Wequicklyoutlinethefunctionalityofthebuttonsinthevisonetoolbarfromlefttoright:
Figure10:visonetoolbar.
newemptynetwork -createanewemptynetworktabinthenetworkpanel
•
opennetworkfromfile-loadanexistingnetworkfromfile
•
savenetworktofile-savethecurrentlydisplayednetworkinthenetworkpaneltoafile
•
zoomout -decreasethezoomlevelofthenetworkpanel
•
zoomlevelcombobox -selectaspecificzoomlevel
•
zoomin-increasethezoomlevelofthenetworkpanel
•
zoomto100% -setthezoomlevelto100%
•
zoomtofitnetwork -automaticallyadjustthezoomleveltoperfectlyfityournetwork
•
zoomtofitall -automaticallyadjustthezoomlevelofallopennetworkstoacommonviewport
•
attributemanager -openstheattributemanager
•
1.3.3 Interaction Modes
Inthetoolbaryoucanswitchbetweenthreedi↵erentinteractionmodestointeractwiththenetwork
panel.
Figure11:Interactionmodesinthetoolbar.
analysismode
•
Inanalysismodeyoucanselectnodesandedges,ordragnodestochangetheirposition.
editmode
•
Ineditmodeyoucanselectnodesandedges,ordragnodestochangetheirposition.
stressmode
•
Instressmodeyoucanimprovelocalstresswhiledraggingnodes,whichisusefulintheexploration
oflargegraphs.
10