Downloads on EES 4760/5760

Resources

Wed, 22 Aug 2018 00:00:00 +0000

Artificial Societies

Thu, 22 Aug 2019 00:00:00 +0000

Reading for Aug. 25

Peter Tyson, “Artificial Societies ,” MIT Technology Review 100(3), 15–17 (Apr., 1997). https://www.ees4760.jmgilligan.org/files/reading/Tyson_Artificial_Societies_1997.pdf

Sugarscape Model from Class #3

Thu, 22 Aug 2019 00:00:00 +0000

Sugarscape Model

NetLogo model for in-class exercises.

ODD Protocol

Thu, 22 Aug 2019 00:00:00 +0000

Documents on ODD protocol

Optional supplementary reading for Sept. 1.

The journal article, V. Grimm et al. (2010). “The ODD protocol: A review and first update” Ecological Modeling 221, 2760–68. . https://www.ees4760.jmgilligan.org/files/odd/Grimm_2010_ODD_update.pdf
A Word document that provides a template for writing ODDs : https://www.ees4760.jmgilligan.org/files/odd/Grimm_2010_odd_template.docx
Lists of scientific publications using agent-based and individual-based models that either do or don’t use the ODD protocol (this appeared as Appendix 1 of the Grimm et al. paper):

Butterfly Model ODD

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model ODD and Scientific Paper

NetLogo model for in-class exercises.

Netlogo model with Butterfly model ODD on the info page , https://ees4760.jmgilligan.org/models/class_04/butterfly_odd.nlogo

Optional supplementary reading.

G. Pe’er, D. Saltz, and K. Frank, “Virtual Corridors for Conservation Management ,” Conservation Biology, 19, 1997–2003 (2005). https://ees4760.jmgilligan.org/files/reading/Peer-VirtualCorridors-2005.pdf

This is the journal paper that developed and reported the butterfly model.

Mushroom Hunt Model

Thu, 22 Aug 2019 00:00:00 +0000

Mushroom Hunt Model (from Chapter 2)

Download the Basic Mushroom-Hunt Model

Butterfly Models

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model for In-Class Exercises on Sept. 3

Download the Basic Butterfly Model
Download the Enhanced Butterfly Model that we wrote in class.

I have made a few changes to the enhanced model that are different from what we did in class:
- I changed the name of the turtles-own variable start-patch to origin to be more concise.
- I changed the equation for the corridor width from $$ \frac{\text{# patches visited}}{\text{sum}(\text{distance-moved})} $$ to $$ \frac{\text{# patches visited}}{\text{mean}(\text{distance-moved})} $$ because that’s what the book uses in Chapter 5.
- I define the turtle to be at the top of a hill when its patch is the highest in a radius of 3 patches, rather than the highest of all its neighbors.
- I add a turtles-own variable at-top? that records whether the turtle is at the top of a hill, and in the to go procedure, I tell the model to stop running if all the turtles are at the top of a hill before it gets to 1000 ticks.

Science with Butterfly Models

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model for In-Class Exercises on Sept. 8

A single ZIP file with all the files https://ees4760.jmgilligan.org/models/class_06/class_06.zip

Or individual files

A butterfly model from Chapter 5:
https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06a.nlogo
A version of the butterfly model with modifications:
https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06b.nlogo
Versions of the butterfly model with code for testing:
- https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06c.nlogo
- https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06c_testing.nlogo
A digital elevation map of real hills
https://ees4760.jmgilligan.org/models/class_06/ElevationData.txt

Culture Dissemination Model with Errors

Thu, 22 Aug 2019 00:00:00 +0000

Fixing Errors in Models

Optimizing Butterfly Model for Mating

Fri, 13 Sep 2019 00:00:00 +0000

Updated Butterfly Model

Butterfly model for optimizing q to maximize mating https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7.nlogo
Elevation data for Butterfly model https://ees4760.jmgilligan.org/models/class_07/ElevationData.txt
BehaviorSpace output for optimizing mating for butterflies starting at the edge of the world: https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7%20optimize-mating-table.csv
BehaviorSpace output for optimizing mating for butterflies starting at different locations: https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7%20optimize-mating-big-table.csv

Flocking Model for Studying Emergence

Thu, 22 Aug 2019 00:00:00 +0000

Modified flocking model for stuying emergence

Butterfly Model for Practicing Observations

Thu, 22 Aug 2019 00:00:00 +0000

Modified butterfly model for practicing observations

Link Demonstration Model

Mon, 01 Jan 2018 00:00:00 +0000

Demonstration model for links

Link demo model

Objectives and Adaptations

Thu, 22 Aug 2019 00:00:00 +0000

Modified business-investor model for testing different objectives and decision strategies

Interaction Models

Thu, 03 Oct 2019 00:00:00 +0000

Telemarketer and Prisoner’s Dilemma models for in-class exercises about

interactions

class_14_models.zip , which contains:
- Prisoner’s Dilemma Models
  - PD_simple.nlogo
  - PD_reciprocity.nlogo
- Behaviorspace Output:
  - PD_simple_experiment table.csv
  - PD_reciprocity_experiment table.csv

Team Project Templates

Mon, 01 Jan 2018 00:00:00 +0000

Templates for programming team-project models

Business Investor Model

Printable PDF
Text file that you can paste into the “info” tab in your NetLogo model.
NetLogo template

Telemarketer Model:

Printable PDF
Text file that you can paste into the “info” tab in your NetLogo model.
Figure for ODD
NetLogo template

Models for Scheduling

Thu, 22 Aug 2019 00:00:00 +0000

Models for in-class exercises on scheduling

class_17_models.zip , which contains:
- Mousetrap models:
  - Mousetrap_Ch14_v1.nlogo
    - Discrete events on integer ticks
  - Mousetrap_Ch14_v2.nlogo
    - Semi-discrete events on fractional ticks
  - Mousetrap_Ch14_v3.nlogo
    - Continuous events, tracking balls in air

Breeding Synchrony:
- Ch_23_4_breeding_synchrony.nlogo

Stochasticity: Stochastic Business Investor

Thu, 22 Aug 2019 00:00:00 +0000

Stochastic business-investor model for in-class exercise

class_18_models.zip , which contains:
- Stochastic Business-Investor model:
  - NetLogo model: business_investor_class_18.nlogo

Collectives: Wild-Dog Models

Thu, 22 Aug 2019 00:00:00 +0000

Wild-dog models for in-class exercises on collectives

class_19_models.zip , which contains:
- Wild-dog model:
  - NetLogo model: wild_dogs.nlogo
  - ODD: wild_dog_odd.pdf
- Behaviorspace output:
  - Varying initialization (number and size of packs at beginning): wild_dogs vary_initialization_pe-table.csv
  - Varying disperser pack parameters (meeting rate and mortality): wild_dogs vary_meeting_disp_mortality_pe-table.csv

Theory Development: Wood Hoopoe Model

Thu, 22 Aug 2019 00:00:00 +0000

Wood Hoopoe breeding models for in-class exercises on theory development

class_21_models.zip , which contains:
- Wood Hoopoe model:
  - NetLogo model: wood_hoopoe_class_21.nlogo
  - ODD: wood_hoopoe_odd.pdf
  - NetLogo model with alternate strategies: wood_hoopoe_strategies.nlogo

Calibration and Parameterization

Thu, 22 Aug 2019 00:00:00 +0000

Wood Hoopoe breeding models for in-class exercises on parameterization and calibration

class_22_models.zip , which contains:
- Wood Hoopoe NetLogo model: Sect20-5_WoodHoopoes_2ndEd.nlogo
- R Scripts to analyze behaviorspace output:
  - process_bs.R
  - analyze_woodhoopoe.R
- Behaviorspace output:
  - Sect20-5_WoodHoopoes_2ndEd Calibration-table.csv

Optional reading for Agent-Based Models in Practice

Thu, 22 Aug 2019 00:00:00 +0000

Optional supplementary reading

Analyzing and Understanding Models

Thu, 22 Aug 2019 00:00:00 +0000

Schelling Segregation Model for In-Class Analysis Exercise

class_24_models.zip , which contains:
- Schelling segregation model: segregation.nlogo

Downloads on EES 4760/5760

Resources

Further Reading about Agent-Based Modeling and a Guide to Computational Tools and Resources

Artificial Societies

Reading for Aug. 25

Sugarscape Model from Class #3

Sugarscape Model

NetLogo model for in-class exercises.

ODD Protocol

Documents on ODD protocol

Optional supplementary reading for Sept. 1.

Butterfly Model ODD

Butterfly Model ODD and Scientific Paper

NetLogo model for in-class exercises.

Optional supplementary reading.

Mushroom Hunt Model

Mushroom Hunt Model (from Chapter 2)

Butterfly Models

Butterfly Model for In-Class Exercises on Sept. 3

Science with Butterfly Models

Butterfly Model for In-Class Exercises on Sept. 8

Or individual files

Culture Dissemination Model with Errors

Fixing Errors in Models

Optimizing Butterfly Model for Mating

Updated Butterfly Model

Flocking Model for Studying Emergence

Modified flocking model for stuying emergence

Butterfly Model for Practicing Observations

Modified butterfly model for practicing observations

Link Demonstration Model

Demonstration model for links

Objectives and Adaptations

Modified business-investor model for testing different objectives and decision strategies

Interaction Models

Telemarketer and Prisoner’s Dilemma models for in-class exercises about

Team Project Templates

Templates for programming team-project models

Business Investor Model

Telemarketer Model:

Models for Scheduling

Models for in-class exercises on scheduling

Stochasticity: Stochastic Business Investor

Stochastic business-investor model for in-class exercise

Collectives: Wild-Dog Models

Wild-dog models for in-class exercises on collectives

Theory Development: Wood Hoopoe Model

Wood Hoopoe breeding models for in-class exercises on theory development

Calibration and Parameterization

Wood Hoopoe breeding models for in-class exercises on parameterization and calibration

Optional reading for Agent-Based Models in Practice

Optional supplementary reading

Analyzing and Understanding Models

Schelling Segregation Model for In-Class Analysis Exercise