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Chris Jewell
covid19uk
Commits
e0f5eb59
Commit
e0f5eb59
authored
Dec 09, 2020
by
Chris Jewell
Browse files
ANalysis as of 2020-12-04
Note: in the actual analysis, the effect of December Tiers was removed.
parent
7497e734
Changes
4
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Inline
Side-by-side
enqueue_pipeline.sh
View file @
e0f5eb59
...
...
@@ -2,9 +2,9 @@
# Enqueues COVID-19 pipelines
CASES_FILE
=
"data/Anonymised Combined Line List 20201
130
.csv"
DATE_LOW
=
"2020-09-
04
"
DATE_HIGH
=
"2020-1
1-27
"
CASES_FILE
=
"data/Anonymised Combined Line List 20201
207
.csv"
DATE_LOW
=
"2020-09-
11
"
DATE_HIGH
=
"2020-1
2-04
"
TEMPLATE_CONFIG
=
template_config.yaml
...
...
inference.py
View file @
e0f5eb59
...
...
@@ -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]
...
...
model_spec.py
View file @
e0f5eb59
...
...
@@ -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
():
...
...
poetry.lock
View file @
e0f5eb59
...
...
@@ -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 = "
eddb85f7bfb3155777dc475eb467582f8caee9a
5"
resolved_reference = "
b7fd2c86e16710d5cd357df2b11b0ffa5ab26ec
5"
[[package]]
name = "geopandas"
...
...
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