Commit a8bfee17 authored by Chris Jewell's avatar Chris Jewell
Browse files

No-tier analysis branch

parent 05991fe8
......@@ -77,7 +77,7 @@ def mcmc(data_file, output_file, config, use_autograph=False, use_xla=True):
gamma0=block0[1],
gamma1=block0[2],
sigma=block0[3],
beta3=block0[4:],
beta3=tf.zeros([5], dtype=DTYPE), # block0[4:],
beta1=block1[0],
xi=block1[1:],
seir=events,
......@@ -99,9 +99,9 @@ def mcmc(data_file, output_file, config, use_autograph=False, use_xla=True):
tfp.bijectors.Exp(),
tfp.bijectors.Identity(),
tfp.bijectors.Exp(),
tfp.bijectors.Identity(),
#tfp.bijectors.Identity(),
],
block_sizes=[1, 2, 1, 5],
block_sizes=[1, 2, 1], #, 5],
),
name=name,
)
......@@ -252,7 +252,7 @@ def mcmc(data_file, output_file, config, use_autograph=False, use_xla=True):
tf.random.set_seed(2)
current_state = [
np.array([0.6, 0.0, 0.0, 0.1, 0.0, 0.0, 0.0, 0.0, 0.0], dtype=DTYPE),
np.array([0.6, 0.0, 0.0, 0.1], dtype=DTYPE), #, 0.0, 0.0, 0.0, 0.0, 0.0], dtype=DTYPE),
np.zeros(
model.model["xi"](0.0, 0.1).event_shape[-1] + 1,
dtype=DTYPE,
......@@ -270,7 +270,7 @@ def mcmc(data_file, output_file, config, use_autograph=False, use_xla=True):
"gamma0": (samples[0][:, 1], (NUM_BURST_SAMPLES,)),
"gamma1": (samples[0][:, 2], (NUM_BURST_SAMPLES,)),
"sigma": (samples[0][:, 3], (NUM_BURST_SAMPLES,)),
"beta3": (samples[0][:, 4:], (NUM_BURST_SAMPLES, 2)),
"beta3": (tf.zeros([1,5], dtype=DTYPE), (NUM_BURST_SAMPLES, 2)), #(samples[0][:, 4:], (NUM_BURST_SAMPLES, 2)),
"beta1": (samples[1][:, 0], (NUM_BURST_SAMPLES,)),
"xi": (
samples[1][:, 1:],
......@@ -309,7 +309,7 @@ def mcmc(data_file, output_file, config, use_autograph=False, use_xla=True):
"gamma0": samples[0][:, 1],
"gamma1": samples[0][:, 2],
"sigma": samples[0][:, 3],
"beta3": samples[0][:, 4:],
"beta3": tf.zeros([samples[0].shape[0], 5], dtype=DTYPE), #samples[0][:, 4:],
"beta1": samples[1][:, 0],
"xi": samples[1][:, 1:],
"events": samples[2],
......
......@@ -17,8 +17,8 @@ for PILLAR in both 1 2
do
for CASE_DATE_TYPE in specimen
do
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}_nl
JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}_notier
JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}_notier"
qsub -N $JOB_NAME covid_pipeline.sge \
--reported-cases "$CASES_FILE" \
--commute-volume "$COMMUTE_VOL_FILE" \
......
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