FishCensus Model

Latest version available at


NetLogo 6 required to use the latest version of the model. Available for free here.

There is a small wiki on Bitbucket.

Checkout the species database where you can download species to use with FishCensus!

... or create and submit your own species.

This model simulates how different fish behaviors affect density estimates in common underwater visual census methods. These include accuracy and precision of estimates and bias due to non-instantaneous sampling. Ultimately, the model can help decide the best method and sampling effort for a real upcoming field assessment.


The model builds upon two previous fish census models, the Reefex model by Watson et al. (1995) and the AnimDens model by Ward-Paige et al. (2010). The simulation of sampling methods (timed transect, stationary point count and random path) is based on the AnimDens model, with the addition of a fixed distance transect, while the inclusion of diver avoidance, behavior changes and count saturation is based on the Reefex model. When compared to both these models, FishCensus features a greater spatial and temporal resolution and more complex and realistic fish movement.

Looking for collaborations! Contact me!

For more information and the full description of the model, please read 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 346C, 58-69. doi: 10.1016/j.ecolmodel.2016.12.011

Sample videos

A species forming small schools.

A species forming large schools.

A species that avoids divers.

A species that is attracted to divers.


The Species Creator interface

The FishCensus model interface


There are several ways you can contribute!



If you are a researcher using underwater visual census and are interested in using FishCensus to help your research, contact me and we can probably think of something together that can benefit the model development and help field test it!

If you are an experienced NetLogo modeller and you like this model, you can help me optimise code and develop new features, so contact me!

Create and submit species

FishCensus relies heavily on well represented species behaviour. Due to the great amount of parameters, it is not easy to find information in the literature that can be used to directly and objectively parameterise a species without any previous contact with it, even though some pattern matching can be achieved with video data:


For this reason, there is a species creator bundled with FishCensus that lets you create your own species, export them to a csv file and then import the file to the main FishCensus model for testing. If you are an expert on a species, or an experienced observer, you can create and share it with the community via the species submission form. If the species parameterisation is well founded and you are confident of its usability, the species is included in the database for others to use and cite any work you have done with it!

Here is a video tutorial with the basics of species creation:

Buy me a beer

If you like FishCensus and want to support development, consider a PayPal donation! I won't stop you.