ANalysis as of 2020-12-04

Note: in the actual analysis, the effect of December Tiers was
removed.

enqueue_pipeline.sh

@@ -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
 

inference.py

@@ -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

@@ -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

@@ -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"