1. Miguel Pessanha Pais Avatar Miguel Pessanha Pais
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FishCensus Model

FishCensus is an agent-based model that simulates underwater visual census of fish populations, a method used worldwide to survey shallow marine and freshwater habitats that involves a diver counting fish species to estimate their density. It can help estimate sampling bias, apply correction factors to field surveys and decide on the best method to survey a particular species, given its behavioural traits, detectability or speed. A modified vector-based boids-like movement submodel is used for fish, and complex behaviours such as schooling or diver avoidance / attraction can be represented.

How it works

The FishCensus model comes with two separate programs. The Species Creator is used to create new fish species or observe/edit existing ones. Species parameters can be exported as a .csv file and imported into the main model where the simulation happens.

In the main FishCensus program, a virtual diver uses a pre-selected survey method (e.g. fixed distance or timed transect, stationary point counts) to count the fish and estimate their density. The true density of fish is pre-determined and known, which allows for the quantification of bias, a measure that is unknown in the field, where determining the true abundance is very difficult.

For a quick start guide, go to the tutorial page of this wiki.

Installation and documentation

FishCensus is programmed in NetLogo, a program and language specifically at building agent-based models. Installation is very easy and straightforward:

  1. Download and install NetLogo 5.3.1;
  2. Get the latest stable release of the FishCensus model from OpenABM;
  3. Get the "rnd" folder from the "required NL extensions folder you find in the model package and move it to your NetLogo 5.3.1/app/extensions folder.
  4. Open the FishCensus.nlogo file to run the model with existing species, or
  5. Open the FishCensus Species Creator.nlogo file to create and export your own species!

If you use this model, please cite the original publication:

Pais, M.P., Cabral,H.N., 2017. Fish behaviour effects on the accuracy and precision of underwater visual census surveys. A virtual ecologist approach using an individual-based model. Ecological Modelling 346, 58-69.

Please check the model page at OpenABM for instructions on how to cite the model itself.

Copyright 2016 Miguel Pessanha Pais

CC BY-NC-SA 4.0

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

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