Predicting paleo-reef distributions

Adaptation of the workflows developed by Tristan Salles that predict reef distribution using the HADCM3 set of climate simulations. This original workflow is found in the folder HADCM3Workflows.

To run with plasim-genie climate output

This is all done in the plasimGenieWorkflows folder.

1. Get present day carbonate locations in getCarbonateLocations.ipynb
2. Get the preferred arrangement of CO² in GMST_CO2.ipynb
3. Get the environmental rasters that biomod reads in the getEnvRasters.py script (not the jupyter notebook). At the moment biomod will read every raster in the folder, so this needs to be re-run everytime you change the set of rasters used by biomod. This is just done through commenting out different raster save lines of code.
4. Use processpared.ipynb to get a csv of all the PARED coral instances that we want to use along with their reconstructed paleo-location.
5. Use runModel.ipynb to run the biomod model, but also to clip the data to shelves, and plot the data. A lot of work is done in this notebook.

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Note: runModel.ipynb calls the two R scripts getEnsembleModel.r and getEnsembleProjection.r