Commit 62f9ec37 authored by Chris Jewell's avatar Chris Jewell
Browse files

Merge branch 'fix-prediction-weekday' into 'master'

Fix for weekday effect in prediction

See merge request !37
parents 45a79675 3df0dd34
......@@ -3,6 +3,7 @@
import numpy as np
import xarray
import pickle as pkl
import pandas as pd
import tensorflow as tf
from covid import model_spec
......@@ -75,11 +76,17 @@ def predict(data, posterior_samples, output_file, initial_step, num_steps):
origin_date = np.array(cases.coords["time"][0])
dates = np.arange(
origin_date + np.timedelta64(initial_step, "D"),
origin_date,
origin_date + np.timedelta64(initial_step + num_steps, "D"),
np.timedelta64(1, "D"),
)
covar_data["weekday"] = xarray.DataArray(
(pd.to_datetime(dates).weekday < 5).astype(model_spec.DTYPE),
coords=[dates],
dims=["prediction_time"],
)
estimated_init_state, predicted_events = predicted_incidence(
samples, initial_state, covar_data, initial_step, num_steps
)
......@@ -89,7 +96,7 @@ def predict(data, posterior_samples, output_file, initial_step, num_steps):
coords=[
np.arange(predicted_events.shape[0]),
covar_data.coords["location"],
dates,
dates[initial_step:],
np.arange(predicted_events.shape[3]),
],
dims=("iteration", "location", "time", "event"),
......
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