IBASAM REPOSITORY

This repository includes the IBASAM simulation model (operating under the Capsis software), along with all the necessary files and scripts to replicate the analyses presented in the paper "IBASAM: a spatially explicit demo-genetic individual-based model for anadromous salmonids (meta)populations", which was published by Lamarins et al. in the journal Individual-based Ecology.

1. CAPSIS folder: contains the executable file capsis-installer-IBASAM-3.0.0.jar to install the software Capsis on your computer and run the IBASAM model. This folder also contains a User Guide that describes how to install Capsis and run IBASAM using the Capsis graphical interface or scripts.

2. RUN_CAPSIS_SCRIPT_MODE folder: contains all the necessary scripts to run the IBASAM model in script mode.

3. GENERATE_CONDITIONS_FILES folder: contains examples of R scripts to generate the river, weir and sea conditions files required to run simulations.

4. CALIBRATION_ABC folder: contains all the scripts required to run the IBASAM model in script mode for a matrix of parameters values for a calibration analysis. 

5. SENSITIVITY_ANALYSIS folder: contains all the scripts required to run the IBASAM model in script mode for a matrix of parameters values for a sensitivity analysis. 

6. IBASAM_Explorer folder: contains a Shiny app to learn more about the model and easily explore simulations results using summary exports.

7. Scorff_observed_data folder: contains observations data on the Scorff needed to compare simulations to observed patterns (e.g. for the calibration analysis).