verfishd 0.2.0

Simulate the vertical fish distribution influenced by physical stimuli

VerFishD is a library to do vertical fish distribution simulations influenced by physical stimuli. It is still in development and not yet ready for production.

Concept

The library uses PhysicalFactor which influence the movement of the fish. They can be created by implement this base class for your own physical factors like temperature, light, oxygen, et cetera. The next step would be to load a StimuliProfile which is a collection of concrete stimuli values. The migration speed is the function to calculate the final vertical movement of the fish. The sign of this function determines the direction of the movement and the absolute value the percentage of fish that will move. All these values are combined in the VerFishDModel which is the main class to run the simulation. The simulation is then triggered by calling the simulate method with the number of time steps to simulate.

Dependencies

To work with .cnv files of CTD casts, the library uses the seabird library. The profile can be loaded by calling StimuliProfile.read_from_cnv(file_path).

Example

https://github.com/marine-data-science/verfishd/blob/752e3501ce62ffe1b563d25e3a7783d529d1aba2/Examples/simple_simulation.py#L5-L46

Installation

pip install verfishd

Ideas for the future

• Combine multiple Stimuli Profiles to do a simulation for a whole day
• Algorithm to determine if simulation can end?