Importing a Pajek Graph

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Contents

File Format

STEM allows users to create a custom graph using a format similar to the Pajek ([1]) format. The PajekNetGraphGenerator, which is available in the graph creation dialogue of STEM, can create user-defined graphs for STEM and is based on this format. The format specification is as follows.

*Vertices [number of nodes]
[node number] [node name] [longitude] [latitude] [additional optional parameters]
...
*Edges
[origin node number] [destination node number] popID [populationID] rate [rate] // spec for migration edges
[containing node number] [contained node number] // spec for containment edges
...

*Vertices

The keyword "*Vertices [number of nodes]" is the starting point for the section, in which each node is described using following format:

[node number] [node name] [longitude] [latitude] [optional parameters]

  • node number – unique node number (1, 2, 3, ...). Successive numbering of nodes is obligatory.
  • node name – unique name consisting of letters a..zA..Z and digits 0..9. The definition of a label is obligatory.
  • longitude, latitude – coordinates of the node. All values can be entered, but real world coordinates are: -180 <= longitude <= 180, 0 <= latitude <= 90. Coordinates are obligatory for STEM.

Optional parameters:

  • 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 Berlin 13.398889 52.500556 popID men popCount 1682900000 popID women popcount 1753500000

*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

*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
3 2

Running the downloadable pajek scenario the map view should appear as shown below.

STEM PajekExample.png

Using the dialog

STEM PajekDialog.png

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