Commit e0f5eb59 authored by Chris Jewell's avatar Chris Jewell
Browse files

ANalysis as of 2020-12-04

Note: in the actual analysis, the effect of December Tiers was
removed.
parent 7497e734
......@@ -2,9 +2,9 @@
# Enqueues COVID-19 pipelines
CASES_FILE="data/Anonymised Combined Line List 20201130.csv"
DATE_LOW="2020-09-04"
DATE_HIGH="2020-11-27"
CASES_FILE="data/Anonymised Combined Line List 20201207.csv"
DATE_LOW="2020-09-11"
DATE_HIGH="2020-12-04"
TEMPLATE_CONFIG=template_config.yaml
......
......@@ -110,7 +110,7 @@ if __name__ == "__main__":
gamma0=block0[1],
gamma1=block0[2],
sigma=block0[3],
beta3=tf.concat([block0[4:6], [0.0]], axis=-1),
beta3=block0[4:],
beta1=block1[0],
xi=block1[1:],
seir=events,
......@@ -142,7 +142,7 @@ if __name__ == "__main__":
tfp.bijectors.Exp(),
tfp.bijectors.Identity(),
],
block_sizes=[1, 2, 1, 2],
block_sizes=[1, 2, 1, 4],
),
name=name,
)
......@@ -296,7 +296,7 @@ if __name__ == "__main__":
tf.random.set_seed(2)
current_state = [
np.array([0.2, 0.0, 0.0, 0.1, 0.0, 0.0], dtype=DTYPE),
np.array([0.6, 0.0, 0.0, 0.1, 0.0, 0.0, 0.0, 0.0], dtype=DTYPE),
np.zeros(
model.model["xi"](0.0, 0.1).event_shape[-1]
# + model.model["beta3"]().event_shape[-1]
......
......@@ -96,12 +96,12 @@ def CovidUK(covariates, initial_state, initial_step, num_steps, priors):
)
def beta3():
return tfd.Sample(
return tfd.Independent(
tfd.Normal(
loc=tf.constant(0.0, dtype=DTYPE),
scale=tf.constant(100.0, dtype=DTYPE),
loc=tf.constant([0.0] * 4, dtype=DTYPE),
scale=tf.constant([1.0] * 4, dtype=DTYPE),
),
sample_shape=covariates["L"].shape[-1],
reinterpreted_batch_ndims=1,
)
def sigma():
......
......@@ -324,7 +324,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "gemlib"
version = "0.3.0"
version = "0.3.1"
description = "GEMlib scientific compute library for epidemic modelling"
category = "main"
optional = false
......@@ -339,7 +339,7 @@ tfp-nightly = "0.12.0.dev20201027"
type = "git"
url = "http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib.git"
reference = "master"
resolved_reference = "eddb85f7bfb3155777dc475eb467582f8caee9a5"
resolved_reference = "b7fd2c86e16710d5cd357df2b11b0ffa5ab26ec5"
[[package]]
name = "geopandas"
......
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