Computational Model Library

The Episim framework builds upon the established transportation simulation MATSim and is capable of tracking agents’ movements within a network and thus computing infection chains. Several characteristics of the virus and the environment can be parametred, whilst the infection dynamics is computed based upon a compartment model. The spread of the virus can be mitigated by restricting the agents’ activity in certain places.

Peer reviewed Lethal Geometry

Kristin Crouse | Published Fri Feb 21 11:27:16 2020

LethalGeometry was developed to examine whether territory size influences the mortality risk for individuals within that territory. For animals who live in territoral groups and are lethally aggressive, we can expect that most aggression occurs along the periphery (or border) between two adjacent territories. For territories that are relatively large, the periphery makes up a proportionately small amount of the of the total territory size, suggesting that individuals in these territories might be less likely to die from these territorial skirmishes. LethalGeometry examines this geometric relationship between territory size and mortality risk under realistic assumptions of variable territory size and shape, variable border width, and stochastic interactions and movement.

The individuals (agents) are programmed to walk randomly about their environment, search for and eat food to obtain energy, reproduce if they can, and act aggressively toward individuals of other groups. During each simulation step, individuals analyze their environment and internal state to determine which actions to take. The actions available to individuals include moving, fighting, and giving birth.

Ger Grouper

Stefani Crabtree | Published Tue Jan 5 18:35:05 2021

A “Ger” is a yurt style house used by pastoralists in Mongolia. This model simulates seasonal movements, fission/fusion dynamics, social interaction between households and how these relate to climate impacts.

Spatial rangeland model

Marco Janssen | Published Tue Jan 22 01:51:09 2019 | Last modified Sat Oct 17 02:03:28 2020

Spatial explicit model of a rangeland system, based on Australian conditions, where grass, woody shrubs and fire compete fore resources. Overgrazing can cause the system to flip from a healthy state to an unproductive shrub state. With the model one can explore the consequences of different movement rules of the livestock on the resilience of the system.

The model is discussed in Introduction to Agent-Based Modeling by Marco Janssen. For more information see https://intro2abm.com/.

This model was developed to test the usability of evolutionary computing and reinforcement learning by extending a well known agent-based model. Sugarscape (Epstein & Axtell, 1996) has been used to demonstrate migration, trade, wealth inequality, disease processes, sex, culture, and conflict. It is on conflict that this model is focused to demonstrate how machine learning methodologies could be applied.

The code is based on the Sugarscape 2 Constant Growback model, availble in the NetLogo models library. New code was added into the existing model while removing code that was not needed and modifying existing code to support the changes. Support for the original movement rule was retained while evolutionary computing, Q-Learning, and SARSA Learning were added.

Peer reviewed FishMob: Interactions between fisher mobility and spatial resource heterogeneity

Emilie Lindkvist | Published Wed Oct 16 09:17:30 2019 | Last modified Tue Jun 23 17:06:15 2020

Migration or other long-distance movement into other regions is a common strategy of fishers and fishworkers living and working on the coast to adapt to environmental change. This model attempts to understand the general dynamics of fisher mobility for over larger spatial scales. The model can be used for investigating the complex interplay that exists between mobility and fish stock heterogeneity across regions, and the associated outcomes of mobility at the system level.

The model design informed by the example of small-scale fisheries in the Gulf of California, Mexico but implements theoretical and stylized facts and can as such be used for different archetypical cases. Our methodological approach for designing the model aims to account for the complex causation, emergence and interdependencies in small-scale fisheries to explain the phenomenon of sequential overexploitation, i.e., overexploiting one resource after another. The model is intended to be used as a virtual laboratory to investigate when and how different levels of mobile fishers affect exploitation patterns of fisheries resources.

The community consequences of intra-specific trait variation (ITV) are a current topic in ecological research. The effects of ITV on species coexistence have, yet, not sufficiently been understood. With this individual-based model we analyzed the effect of intra-specific variation in movement by mimicking variation found in ground-dwelling rodents and analyzing how such variation affects inter-specific differences in competitive ability (i.e. foraging efficiency) and temporary coexistence. The movement algorithm and behavioral plasticity was adapted from existing algorithms and current ecological literature. As a measure for temporary coexistence, we analyzed the time until one of the species went extinct.

Our aim is to show effects of group living when only low-level cognition is assumed, such as pattern recognition needed for normal functioning, without assuming individuals have knowledge about others around them or warn them actively.
The model is of a group of vigilant foragers staying within a patch, under attack by a predator. The foragers use attentional scanning for predator detection, and flee after detection. This fleeing action constitutes a visual cue to danger, and can be received non-attentionally by others if it occurs within their limited visual field. The focus of this model is on the effectiveness of this non-attentional visual information reception.
A blind angle obstructing cue reception caused by behaviour can exist in front, morphology causes a blind angle in the back. These limitations are represented by two visual field shapes. The scan for predators is all-around, with distance-dependent detection; reception of flight cues is limited by visual field shape.
Initial parameters for instance: group sizes, movement, vision characteristics for predator detection and for cue reception. Captures (failure), number of times the information reached all individuals at the same time (All-fled, success), and several other effects of the visual settings are recorded.

This model implements a classic scenario used in Reinforcement Learning problem, the “Cliff Walking Problem”. Consider the gridworld shown below (SUTTON; BARTO, 2018). This is a standard undiscounted, episodic task, with start and goal states, and the usual actions causing movement up, down, right, and left. Reward is -1 on all transitions except those into the region marked “The Cliff.” Stepping into this region incurs a reward of -100 and sends the agent instantly back to the start (SUTTON; BARTO, 2018).

CliffWalking

The problem is solved in this model using the Q-Learning algorithm. The algorithm is implemented with the support of the NetLogo Q-Learning Extension

FNNR-ABM

Judy Mak | Published Thu Feb 28 04:26:47 2019 | Last modified Sat Dec 7 23:19:51 2019

FNNR-ABM is an agent-based model that simulates human activity, Guizhou snub-nosed monkey movement, and GTGP-enrolled land parcel conversion in the Fanjingshan National Nature Reserve in Guizhou, China.

Quick-start guide:
1. Install Python and set environmental path variables.
2. Install the mesa, matplotlib (optional), and pyshp (optional) Python libraries.
3. Configure fnnr_config_file.py.

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