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Finish augmented dataset at 0.1 degree resolution:
Pull in all static variables.
Pull in immunity layer.
Create layer for whether there has been an outbreak in the region in the last year, as a first pass. (In a future iteration this could be something like distance to nearest outbreak in the last year.)
Outcome layer representing whether there has been an outbreak in the pixel in the month following the selected date
For example, if the random date is January 19th 2023, the lag data represents three months up until this day. We need to know if an outbreak happened from January 20th - February 19th 2023.
Note to save time, I implemented this on the polygon basis instead of by pixel (20240305)
Data steps for ARC model
Filter to South Africa and Eswatini
Aggregate to ADM level 2
Average NDVI, weather, forecasts
Sum taxa population
Most likely remove slope and aspect - they become less relevant/interpretable at the ADM level
Average immunity? (Note, the immunity layer could potentially be regenerated at the ADM level and have the parameters tuned in the model)
Make area of the polygon one of the fields
We can remove forecast fields beyond 1 month ahead.
Model pipeline
Train/validation split randomly by day and ADM
Fix xgboost model
Use "base_margin" in xgboost to account for probability per unit area.
Validation report
Prediction
Some of these steps can use/adapt existing functions from the training pipeline.
Download all data for past three months
Transform data, including steps to scale to 0.1 degrees, calculate lagged anomalies against stored historical values.
Augment and aggregate into ADM regions
Run predictions using stored model object
Return a shapefile
The text was updated successfully, but these errors were encountered:
In case it affects your efforts on the static layers @n8layman, note we had said that we would most likely remove slope and aspect from the final model
Training
Prediction
Some of these steps can use/adapt existing functions from the training pipeline.
The text was updated successfully, but these errors were encountered: