# Importing a Pajek Graph

## 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] // spec for a new node [node number] [node URI] // spec for reference to existing node ... *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 ...

## Node Format

The keyword "*Vertices [number of nodes]" is the starting point for the nodes section. New nodes and references to existing nodes can be defined. The formats are as follows.

### New Node

**[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.
- longitude, latitude – coordinates of the node. All values can be entered, but real world coordinates are: -180 <= longitude <= 180, 0 <= latitude <= 90.

**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

### Node Reference

**[node number] [node URI]:**

- node number – unique node number (1, 2, 3, ...). Successive numbering of nodes is obligatory.
- node URI – URI of the node in STEM. If the URI starts with
*stem://org.eclipse.stem/node/geo/region/*, this prefix can be omitted.

**Examples:**

1 stem://org.eclipse.stem/node/geo/region/FR-IF 1 FR-IF

## Edges Format

The keyword "*Edges" is the starting point for the edges section. Two types of edges can be described migration edges and containment edges. The formats are as follows.

### Migration Edges

**[origin node number] [destination node number] popID [populationID] rate [rate]:**

- origin node number – number of the node the population migrates from. Has to be defined as node number in *Vertices.
- destination node number – number of the node the population migrates from. Has to be defined as node number in *Vertices.
- populationID – defines the ID of the migrating population.
- rate - number population members migrating per day.

**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.

**Example:**

1 2 popID beef rate 1.0 date 2012-01-01 rate 10.0

### Containment Edges

**[containing node number] [contained node number]:**

- containing node number – number of the node that contains the other node. Has to be defined as node number in *Vertices.
- contained node number – number of the node that is contained by the other node. Has to be defined as node number in *Vertices.

## 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.

## Using the 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