Code for reproducible AMLR reporting
The 'data' folder for this repository and these reports contains raw, unpublished data, and thus is not included in the repo (i.e., it is git-ignored). It can be found in this Drive link (NOAA internal only)
Notes for updating the report and data files each year
Make a copy of the past year's qmd file...
Pinniped-specific updates to the files in the 'data' folder:
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Generate a new pup fate file ('cs_afs_pup_fate.csv'), by running the script 'amlr-pinnipeds-database-scripts/ad-hoc/pup_fate.R'
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Update 'pred_ftr_krill_performance.csv'. Columns: 'Duration': SSAFS average trip length across first 6 trips (C1 value); 'Krill': value from seabird work; 'Success': the mean weight of pups collected during the 2nd CCAMLR pup weight study
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Extract any GPS points from Mk10s, and add to 'trackdata.csv'
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Add SSAFS pup counts to 'offsprint_data.csv'. Add the CS Cape-wide pup count to the 'Data' column, in a row with Site "CS" and Index "AFS-CS". Also add any new STI (San Telmo Islets) and SSI (South Shetland) counts, replacing "CS" with the relevant code (i.e., "STI" or "SSI").
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