List of commands with short explanation

1 Programs for Analysisand Visualizationof Very Large NetworksReference ManualList of commands with short explanationversion Mrvar and Vladimir BatageljLjubljana, October 28, 2020c 1996, 2020 A. Mrvar, V. Batagelj., Free for noncommercial version October 1, 2003 Andrej MrvarFaculty of Social SciencesUniversity of Ljubljana, BatageljDepartment of Mathematics, FMFU niversity of Ljubljana, Data objects83 Main Window .. 664 Draw Window Window Draw Tool.. 8315 Exports to EPS/SVG/X3 .. in EPS, SVG, X3D, and VRML Defaults Window .. pictures to EPS/SVG defining parameters in input Unicode in Pajek s pictures.

2 936 Using Macros is a Macro? .. to record a Macro? .. to execute the Macro? .. of macros available in installation file .. prepared for genealogies and other acyclic networks prepared for computing derived kinship relations . session .. command .. last command .. constant(s) reported by last command to Scalar(s) .. 997 Blockmodeling .. ofMDLfiles .. blocks .. blocks (clustering) .. model (up) .. model with symmetric clusters (down) .. path .. chain .. standard model for .. 1048 Colors inPajek1059 CitingPajek1072 Pajek Manual31 PajekPajekis a program, for Windows, for analysis and visu-alization oflarge networkshaving some thousands or evenmillions of vertices.

3 In Slovenian language the wordpa-jekmeans spider. The latest version ofPajekis freelyavailable, for noncommercial use, at its home page: started the development ofPajekin November im-plemented in Delphi (Pascal). Some procedures were contributed by Matja z Za-ver main motivation for development ofPajekwas the observation thatthere exist several sources of large networks that are already in provide tools for analysis and visualization of such net-works: collaboration networks, organic molecule in chemistry, protein-receptorinteraction networks, genealogies, Internet networks, citation networks, diffusion(AIDS, news, innovations) networks, data-mining (2-mode networks), etc.

4 Seealso collection of large networks at: design ofPajekis based on our previous experiences gained in devel-opment of graph data structure and algorithms libraries Graph and X-graph, col-lection of network analysis and visualization programs STRAN, RelCalc, Draw,Energ, and SGML-based graph description markup language a special editions of memory consumption is much lower. For the same network they need atleast 2-3 times less physical memory thanPajek. Operations that are memoryintensive ( generating random networks, extracting, shrinking,..) are alsofaster. In the rest of the manual commands that are specific toPajek-XXLandPajek-3 XLare written in brown font details onPajek-XXLandPajek-3 XLsee: its mirror: Mrvar and V.

5 / October 28, 20204 Pajek ManualFigure 1:Pajek/Spidercut-outreductionlocalgloba lhierarchycontextinter-linksFigure 2:Approaches to deal with large networksThe main goals in the design ofPajekare: to support abstraction by (recursive)decompositionof a large network intoseveral smaller networks that can be treated further using more sophisticatedA. Mrvar and V. / October 28, 2020 Pajek Manual5methods; to provide the user with some powerfulvisualizationtools; to implement a selection ofefficient(subquadratic)algorithmsfor analysisof large can:findclusters (components, neighbourhoods of impor-tant vertices, cores, etc.) in a network,extractvertices that belong to the sameclusters andshowthem separately, possibly with the parts of the context (detailedlocal view),shrinkvertices in clusters and show relations among clusters (globalview).

6 Besides ordinary (directed, undirected, mixed) networksPajeksupports alsomulti-relational networks,2-mode networks(bipartite (valued) graphs networksbetween two disjoint sets of vertices), andtemporal networks(dynamic graphs networks changing over time).A. Mrvar and V. / October 28, 20206 Pajek ManualFigure 3:PajektextbookThis manual provides short explanations of all procedures implemented in thelast version ofPajek. The novice users we advise to read thePajektextbook[31]de Nooy W., Mrvar A., Batagelj V. (2018)Exploratory Social Net-work Analysis WithPajek. Revised and Expanded Edition for Up-dated Software. Third Edition. Structural Analysis in the Social Sci-ences 46, Cambridge University Press, an overview ofnetwork analysis withPajeksee the NICTA workshop slidesA.

7 Mrvar and V. / October 28, 2020 Pajek Manual7[5].A. Mrvar and V. / October 28, 20208 Pajek Manual2 Data objectsInPajeksix types of objects are used:Figure 4:Pajek s Main main objects (vertices and lines). Default extension:. can be presented on input file in different ways: using arcs/edges ( 1 2 line from 1 to 2) using arcslists/edgeslists ( 1 2 3 line from 1 to 2 and from 1 to 3) matrix format UCINET, GEDCOM, chemical formats..Additional information for network drawing can be included in input file aswell. This is explained in the section Exports to EPS/ they tell for each vertex to which class vertex belong.

8 Defaultextension:. reordering of vertices. Default extension:. subset of vertices ( one class from partition). Default exten-sion:. hierarchically ordered vertices. Example:A. Mrvar and V. / October 28, 2020 Pajek Manual9 Rootg1 g2g11 g12 v5,v6,v7v1,v2 v3,v4 Root has two subgroups g1 and g2. g2 is a leaf cluster with verticesv5,v6 and v7. g1 has two subgroups g11 and g12.. Default extension:. they tell for each vertex some numerical property (real number).Default extension:. double clicking on selected network, partition,.. you can show the objecton procedures inPajek s main window (see Figure 4) are organized accord-ing to the types of data objects they use as , partitions and vectors can be used to store properties of verticesmeasured in different scales: ordered, nominal (categorical) and 5:Spider web; Photo: Vladimir Mrvar and V.

9 / October 28, 202010 Pajek ManualTable 1: List of time events following events happen whentime pointtstartsTEtend events following events happen whentime pointtis finishedAVvnsadd vertexvwith labelnand propertiessHVvhide vertexvSVvshow vertexvDVvdelete vertexvAAuvsadd arc(u,v) with propertiessHAuvhide arc(u,v)SAuvshow arc(u,v)DAuvdelete arc(u,v)AEuvsadd edge(u:v) with propertiessHEuvhide edge(u:v)SEuvshow edge(u:v)DEuvdelete edge(u:v)CVvschange vertex property change property of vertexvtosCAuvschange arc property change property of arc(u,v)tosCEuvschange edge property change property of edge(u:v)tosCTuvchange type change (un)directedness of line(u,v)CDuvchange direction of arc(u,v)PEuvsreplace pair of arcs(u,v)and(v,u)by single edge(u:v) with propertiessAPuvsadd pair of arcs(u,v)and(v,u) with propertiessDPuvdelete pair of arcs(u,v)and(v,u)EPuvsreplace edge(u:v)by pair of arcs(u,v)and(v,u) with propertiess3 Main Window FileInput/Output manipulation with the six data objects.

10 Network N Read Read network from Ascii/Unicode UTF8 file. Read Time Events Read temporal network described using timeevents. See Table of propertiesscan be empty as well. If several edges (arcs) canconnect two vertices, additional tag like:k(k-th line) must be given toA. Mrvar and V. / October 28, 2020 Pajek Manual11determine to which line the command applies. commandHE:314 37results in hiding the third edge connecting of time network described using time events:*Vertices 3*EventsTI 1AV 2 "b"TE 3HV 2TI 4AV 3 "e"TI 5AV 1 "a"TI 6AE 1 3 1TI 7SV 2AE 1 2 1TE 7DE 1 2DV 2TE 8DE 1 3TE 10HV 1TI 12SV 1TE 14DV 1 See also other possibility: description of time network using time in-tervals.