Commit 66841afc authored by Chris Jewell's avatar Chris Jewell
Browse files

Analysis code as of 2020-11-20.

CHANGES:

1. update date and data name in enqueue_pipeline.sh
2. update infection time initialisation in model_spec.py
parent 107186d1
......@@ -2,9 +2,9 @@
# Enqueues COVID-19 pipelines
CASES_FILE="data/Anonymised Combined Line List 20201117.csv"
DATE_LOW="2020-08-21"
DATE_HIGH="2020-11-13"
CASES_FILE="data/Anonymised Combined Line List 20201123.csv"
DATE_LOW="2020-08-28"
DATE_HIGH="2020-11-20"
TEMPLATE_CONFIG=template_config.yaml
......@@ -15,7 +15,7 @@ switch-gpu
for PILLAR in both 1
do
for CASE_DATE_TYPE in specimen report
do
do
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}
JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"
qsub -N $JOB_NAME covid_pipeline.sge \
......
......@@ -66,8 +66,8 @@ def impute_censored_events(cases):
:returns: a MxTx3 tensor of events where the first two indices of
the right-most dimension contain the imputed event times.
"""
ei_events, lag_ei = impute_previous_cases(cases, 0.21)
se_events, lag_se = impute_previous_cases(ei_events, 0.28)
ei_events, lag_ei = impute_previous_cases(cases, 0.25)
se_events, lag_se = impute_previous_cases(ei_events, 0.5)
ir_events = np.pad(cases, ((0, 0), (lag_ei + lag_se - 2, 0)))
ei_events = np.pad(ei_events, ((0, 0), (lag_se - 1, 0)))
return tf.stack([se_events, ei_events, ir_events], axis=-1)
......
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