Importing a Pajek Graph

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PajekNetGraphGenerator Example Project

STEM allows users to create a custom graph using a format similar to the Pajek ([1]) format. The PajekNetGraphGenerator allows creating user-defined graphs for STEM and is based on this format, which is specified below. The PajekNetGraphGenerator is available in the graph creation dialogue of STEM. Please see the page Creating a new Graph for information on using this dialog.

Contributors

The PajekNetGraphGenerator was created and developed by the Department of Biological Safety of the Federal Institute for Risk Assessment in Germany.

Armin A. Weiser, Matthias Filter, Christian Thöns
Dept. Biological Safety 
Federal Institute for Risk Assessment
12277 Berlin
Germany

PajekNetGraphGenerator and the STEM-related format extension to Pajek

The following reserved words are supported in the current Pajek Import implementation:

*Vertices n

  • n denotes the number of vertices in the graph.

In STEM nodes are the equivalent of vertices. The keyword "*Vertices n" is the starting point for the section, in which each vertex is described using following format:

vertexnum label x y [z] [shape] [additional optional parameters]

  • vertexnum – vertex number (1; 2; 3 : : : n). Successive numbering of vertices/nodes is obligatory.
  • label – if label starts with character a..zA..Z or 0..9 first blank determines end of the label (e.g., vertex1), labels consisting of more words must be enclosed in pair of special characters (e.g., ”vertex 1”). The definition of a label is obligatory.
  • x, y, z – coordinates of vertex. The z coordinate is ignored in STEM. In Pajek the coordinates have values between 0 and 1, for STEM the values are not limited. x and y coordinates are obligatory for STEM.
  • shape – shape of object which represents vertex. The following shapes are supported by the PajekNetGraphGenerator: triangle, cross, ellipse, box, diamond. In STEM ellipse is represented as circle and box and diamond both are represented as box. box is the default value.

Additional optional parameters:

  • s_size – size of the node. The default size is given by the parameter “Default Area” within the PajekNetGraphGeneratorImpl dialog in STEM. For STEM the size of the node is not limited. Overlaps of nodes are not checked by the importer, they are allowed.
Example: 1 ”vertex one” 0.3456 0.1234 0.5 ellipse s_size 0.1

Parameters only valid in STEM (these parameters are ignored by Pajek):

  • popid – identifier of a population of the node. This parameter may be used repeatedly.
  • popcount – number of individuals living in the node. This parameter may be used repeatedly. The associated popid is the last mentioned one.
Example: 1 ”vertex one” 0.3456 0.1234 0.5 ellipse s_size 0.1 popid human popcount 24 popid anopheles popcount 1000


*Edges

The keyword "*Edges" is the starting point for the edges section. Each edge is described using the following format:

v1 v2 [borderlength] [additional optional parameters]

  • v1 – initial vertex number. The definition of v1 is obligatory. v1 has to be defined as node (see above: vertexnum).
  • v2 – terminal vertex number. The definition of v2 is obligatory. v2 has to be defined as node (see above: vertexnum).
  • borderlength – defines the borderlength for CommonBorderEdges

Additional optional parameters:

Parameters only valid in STEM (these parameters are ignored by Pajek):

  • popid – identifier of a population migrating on the edge. This parameter may be used repeatedly. If this parameter and additionally “rateab” or “rateba” is set at least once then a MigrationEdge will be specified in STEM, otherwise a CommonBorderEdge will be defined.
  • rateba – fraction of the population in node v2 migrating over the edge to the node v1 in a given time period. This parameter may be used repeatedly. The associated popid is the last mentioned one. The default value is 0.
Example: 1 2 popid human rateab 0.2 rateba 0.1 popid anopheles rateab 0.5 rateba 0.1

Example files

In the downloadable project, you will find some examples that may be imported into STEM:

  • CC.NET_2stem.net
  • 1.NET_2stem.net

The filename extension ".net" is not mandatory.

Using the dialog

STEM PajekDialog.png