What is 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.
- How does IBASAM work?
IBASAM is made of 8 submodels representing fundamental biological processes :
- Reproduction and reddcreation
- Emergence from the redds and individual birth
- Genetic coding and transmission
It also includes 2 environmental submodels :
- River climate (Water temperature and flow)
- 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.
- How to use IBASAM?
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.
- What is IBASAM’ goal?
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.
More detailed explanations (processes, installation procedure,…), are provided in the Wiki.
This work is financed under the AFB-INRA conventions.
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
This project is licensed under the terms of the GNU General Public License GPLV3.0.