A package for running multiple simultaneous instances of the Atlantis model from a Docker image, as well as updating parameters in an easy manner. It has basic plotting functions for a quick look at the output of several runs.
Current functions included in the package:
- update_prm.R: simple way of updating parameters with a single value.
- adv_update_prm.R: function that changes parameters to which multiple values are assigned (e.g., diet matrix).
- run_docker_instances.R: a function that starts a Docker container for each input file (limited to biology.prm for now). This requires a small modification of the Run.sh file to include a variable input file (
$PRM_FILE) and an output file ($OUTPUT_DIR), like so:
atlantisMerged -i final_with_ice_input_v2.nc 0 -o output_f_.nc -r EA_run.prm -f EA_force.prm -p EA_physics.prm -b $PRM_FILE -h EA_harvest_nofishing.prm -s AntarcticGroups_v2_basicfoodweb.csv -d $OUTPUT_DIR -m EA_migrations.csv
- massplot.R, rel_mass_plot.R: plotting functions for comparing output from multiple instances.
- get_metric: extracts parameters (input files) and final biomass values (output files) to create a dataset for later analysis.
- optimise_bayesian (WIP): trial version of a small calibration system for Atlantis parameters. It uses Bayesian optimisation to find ideal parameter value based on previous runs.
- whole_shebang (WIP): trial version of self-updating process for Atlantis calibraiton (optimises parameter -> updates input file -> runs updated files in Docker -> optimises parameter, and so on).
- More plotting options for PREBAL checks
- Function for automated calibration of most influential biological parameters