Traits

Contents:

• Traits: collection of customizable dynamically changing attributes.

• Specification: how to define custom attributes.

• Text encoding: format of traits utilized in csv files.

• Examples

Introduction

Synopsis

Traits: collection of customizable dynamically changing attributes.

In EpiHiper the notion of configurable trait collections allows one to associate a custom list of dynamically changing attributes to certain model components. This effectively allows the user to extend the state of the system. Currently EpiHiper allows trait collections for:

• Nodes: The attribute nodeTrait provides for custom extension of each node’s state.

• Edges: The attributes targetActivity, sourceActivity, and edgeTrait provide for custom extensions of each edge’s state:

  • targetActivity: detailed information about the activity of the target node of an edge.

  • sourceActivity: detailed information about the activity of the source node of an edge.

  • edgeTrait: detailed information about the edge itself or its location.

Internally, EpiHiper represents trait collections using a suitably defined bit-field, a fact that will be transparent to the modeler, the only exception being the case of too high trait space complexity causing a bit overflow error.

Specification

Synopsis

Specification: how to define custom attributes.

To define these trait collections, the following syntax is used:

trait:   traitId list(feature) [annotation]
feature: featureId list(enum) default [annotation]
enum:    enumId [annotation]

The trait collections can be specified in several locations (Contact Network, Initialization, Interventions, and Traits). New features can be added to a trait in any of these locations. However, modifying a previously defined feature is not allowed and will cause an error. Identical definitions of the same feature in multiple places are allowed.

Here featureId is the unique id of a feature within the specified trait collection; enumId is a unique identifier within the scope of a feature; a default value must be provided for each feature so that the state will be well defined at the beginning of any simulation; furthermore optional annotation may be provided

The normative JSON schema can be found at:

• trait

• feature

• enum

Text encoding

Synopsis

Text encoding: format of traits utilized in csv files.

Text encoding of traits is is required for text format of the Contact Network.

featureIndex_1:enumIndex_1|featureIndex_2|enumIndex_2, ..., featureIndex_n|enumIndex_n

Here the index starts with 1 for the first feature or enum defined in JSON according to the schema. If a feature is omitted in the encoding the default value is used.

Examples

JSON activity trait encoding:

"activityEncoding": {
  "id": "activityTrait",
  "features": [
    {
      "id": "activityType",
      "default": "other",
      "enums": [
        {
          "id": "home"
        },
        {
          "id": "work"
        },
        {
          "id": "shop"
        },
        {
          "id": "other"
        },
        {
          "id": "school"
        },
        {
          "id": "college"
        },
        {
          "id": "religion"
        }
      ]
    }
  ]
}

Text encoding of activity type work based on the above described activity trait:

1:2