This readme.txt file was generated on 2019 09 25 by Maxime Vaugeois


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GENERAL INFORMATION
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1. Title of Dataset 

  Individual-Based-Model used in "Population context matters : predicting effects of metabolic stress mediated by food availability and predation with an agent- and energy budget-based model"

2. Author Information


  Principal Investigator Contact Information
        Name: Vaugeois Maxime
           Institution: University of Minnesota, Department of Ecology, Evolution, and Behavior 
           Address: 406 Ecology building, 1987 Upper Buford Circle, Saint Paul, MN 55108
           Email:mvaugeoi@umn.edu
	   ORCID:

  Associate or Co-investigator Contact Information
        Name:Forbes Valery, E.
           Institution: University of Minnesota, Department of Ecology, Evolution, and Behavior 
           Address:123 Snyder Hall, 1475 Gortner Ave, St. Paul, MN 55108
           Email:veforbes@umn.edu
	   ORCID:

  Associate or Co-investigator Contact Information
           Name:Venturelli Paul, A.
           Institution: Ball State University, Department of Biology
           Address: Ball State University, Muncie IN 47306
           Email:paventurelli@bsu.edu
	   ORCID:

  Associate or Co-investigator Contact Information
        Name:Accolla Chiara
           Institution: University of Minnesota, Department of Ecology, Evolution, and Behavior 
           Address: Ecology building, 1987 Upper Buford Circle, Saint Paul, MN 55108
           Email:caccolla@umn.edu
	   ORCID:

  Associate or Co-investigator Contact Information
        Name:Hummel Stephanie, L.
           Institution: US Fish & Wildlife Service
           Address: Bloomington, Minnesota, USA
           Email:stephanie_hummel@fws.gov
	   ORCID:



3. Information about funding sources:

  	United States Fisheries and Wildlife Service - Cooperative Agreement Award F17AC00269



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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the model: 
	This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
	This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
	See the GNU General Public License for more details (<http://www.gnu.org/licenses/>).


2. Links to publications that cite or use the model: 
	Vaugeois M., Venturelli P. A., Hummel S. L., Accolla C. and Forbes V. E., 2019. Population context matters: predicting effects of metabolic stress me-diated by food availability and predation with an agent- and energy budget-based model. https://doi.org/10.1016/j.ecolmodel.2019.108903


3. Recommended citation for the model: 
 Vaugeois, Maxime; Accolla, Chiara; Venturelli, Paul A; Forbes, Valery E; Hummel, Stephanie L. (2019). Individual-Based-Model used in "Population context matters: predicting effects of metabolic stress mediated by food availability and predation with an agent- and energy budget-based model". Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/v3rj-n159. 



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DATA & FILE OVERVIEW
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1. File List
  	The FHM DEB-IBM folder contains one xml file, "pom.xml" which details some libraries versions, and 3 sub-folders: src; data; target.
  		- src countains 4 sub-folders containing different source code of the model.
			+ environment contains codes regarding the modelling of space.
			+ miscellaneous contains a code that is called in other codes to shuffle positions or individuals.
			+ observer contains a code that is used to make observation of the simulations.
			+ species.Fish contains all the processes that were modeled (Detailed in the TRACE documentation)
			+ species.shared contains codes that were called in other codes
  		- data contains one sub-folder, named input, containing xml files containing parameters that are passed to the model. 
  		- target contains the .jar file that was compiled using MAVEN.



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METHODOLOGICAL INFORMATION
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1. Description of methods used for the model:
	The model uses a DEB-IBM approach and is developed in Java using the "SimAquaLife" framework, which is an individual-based, process-oriented framework for simulating aquatic life. 

2. Instrument- or software-specific: 
	We used Eclipse (www.eclipse.org), which is a Java integrated development environment to develop the code.

3. How to run the code: 
	For building the project, you will need to import third-party libraries. 
	You will need to download SimAquaLife 2.0 (https://gitlab.irstea.fr/SimAquaLife/SimAquaLife/uploads/1bedae420880f3871144deb370a110e8/simaqualife-2.0.jar) and add it to your project dependencies. 

	The model can be run using "Run" in eclipse with the following "Run Configuration": 
		- Main class: fr.cemagref.simaqualife.pilot.gui.SwingPilot
		- Argument: -simDuration 7300 -simBegin 151 -timeStepDuration 1 -groups data/input/FHM_explo_one_zone2.xml -env data/input/River_one_zone.xml -observers data/input/obs_min.xml -RNGStatusIndex 1

	The model can also be run from the java file in the target folder which was obtained after compilation with MAVEN. To compile "Run as" "Maven Build" with Goals: package bundle:bundle

4. Documentation: 
	A TRACE documentation can be find in the files. This document details the conceptual model and the code development.