This repository contains code for the RAIMBOW (Risk Assessment Integration for Mitigating Bycatch of Whales) project. Code for various pieces of the project are divided into folders:
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prep: Basic prep steps for analyses, such as creating grid cell - info keys and defining Regions. Also includes Grid5km_landerase.R, a script to erase land from Blake's 5km equal area grid, and save the resulting object for future use in whale scripts.
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JS_OceanVisions: Code used to create plots of Jameal's April 2019 OceanVisions presentation
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blue_whale: Files and code for overlaying blue whale predictions (Abrahms et al 2019) onto the 5km grid using overlay method (areal interpolation)
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humpback_risk: Files and code used to determine the risk of entanglement for humpbacks in the Dungeness Crab fishery off the US west coast.
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tradeoffs: Tradeoff analyses for humpback and blue whale entanglement risk and Dungeness Crab fishery activity
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whalepreds_aggregate: Functions to summarize whale predictions by specified time interval. DO NOT EDIT; any edits should be done in the whale-model-prep repository and copied over
Other files include:
- User_script_local.R: Script for determining whom is running the code (user info used to set appropriate file paths); sourced in relevant files
Files in humpback_risk are for Forney et al. (in prep)