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IBASAM

A demo-genetic individual-based model for Atlantic salmon populations

ibasam

IBASAM (Individual Based Atlantic Salmon Model) is an individual-based demo-genetic model developed to simulate S. salar population dynamics in southern European populations.

IBASAM is made of 8 submodels representing fundamental biological processes :

  1. Reproduction and reddcreation
  2. Emergence from the redds and individual birth
  3. Genetic coding and transmission
  4. Growth
  5. Survival
  6. Smoltification
  7. Maturation
  8. Migrations

It also includes 2 environmental submodels :

  1. River climate (Water temperature and flow)
  2. Ocean climate

For the sake of conciseness, all submodels are not extensively justified here. Please see Wiki and Piou et al. (2012) for further explanations and graphics of some of the mathematical functions used.

The IBASAM model was developed in C++ and interfaced as a shared library for R (R Development Core, 2010) to make easy the statistical analyses of model outputs. The C++ source codes and R scripts to create and use the model as R package are available online on Github. More detailed explanations are provided in the Wiki.

Installation procedure

IBASAM is a cohesive and novel tool to assess the effect of potential stressors on evolutionary demography of Atlantic salmon. It includes a demo-genetic structure coupled with the explicit representation of individual variability and complex life histories.

Contribution guidelines for this project

Contents of the folder

References

Piou, C., Taylor, M. H., Papaïx, J., & Prévost, E. (2015). Modelling the interactive effects of selective fishing and environmental change on Atlantic salmon demogenetics. Journal of Applied Ecology, 52(6), 1629-1637. Link

Piou, C., Prévost, E. (2013). Contrasting effects of climate change in continental vs. oceanic environments on population persistence and microevolution of Atlantic salmon. Global Change Biology, 19 (3) : 711-723. Link

Piou, C. & Prévost, E. (2012) A demo-genetic individual-based model for Atlantic salmon populations: Model structure, parameterization and sensitivity. Ecological Modelling, 231, 37–52. Link

License

This project is licensed under the terms of the GNU General Public License GPLV3.0.