Commit b3635b3b authored by Chris Jewell's avatar Chris Jewell
Browse files

Tune MCMC for latest data.

parents 952cbfb1 03d9c5dd
......@@ -11,7 +11,7 @@ ProcessData:
CasesData:
input: csv
address: data/Anonymised Combined Line List 20210426.csv
address: data/latest_line_list.zip
pillars:
- Pillar 1 # Capability to filter Pillar 1 and 2 testing data from PHE confidential line listing
measure: specimen # Capability to filter date of test report from PHE confidential line listing
......@@ -31,14 +31,14 @@ Mcmc:
occult_nmax: 15 # Max number of occults to add/delete per metapop/time
num_event_time_updates: 380 # Num event and occult updates per sweep of Gibbs MCMC sampler.
num_bursts: 100 # Number of MCMC bursts of `num_burst_samples`
num_burst_samples: 50 # Number of MCMC samples per burst
num_burst_samples: 200 # Number of MCMC samples per burst
thin: 20 # Thin MCMC samples every `thin` iterations
num_adaptation_iterations: 1000
ThinPosterior: # Post-process further chain thinning HDF5 -> .pkl.
start: 3000
start: -10000
end:
by: 4
by: 10
Geopackage: # covid.tasks.summary_geopackage
base_geopackage: data/UK2019mod_pop.gpkg
......
......@@ -12,11 +12,11 @@
#$ -S /bin/bash
#$ -P chicas
#$ -q medium
#$ -q short
#$ -l ngpus=1
# -l ncpus=4
#$ -l h_vmem=64G
#$ -l h_rt=24:00:00
#$ -l h_rt=10:00:00
#$ -j y
#$ -cwd
#$ -M c.jewell@lancaster.ac.uk
......
......@@ -30,28 +30,19 @@ Mcmc:
dmax: 84 # Max distance to move events
nmax: 25 # Max num events per metapopulation/time to move
m: 1 # Number of metapopulations to move
occult_nmax: 8 # Max number of occults to add/delete per metapop/time
occult_nmax: 16 # Max number of occults to add/delete per metapop/time
num_event_time_updates: 380 # Num event and occult updates per sweep of Gibbs MCMC sampler.
num_bursts: 100 # Number of MCMC bursts of `num_burst_samples`
num_burst_samples: 50 # Number of MCMC samples per burst
num_burst_samples: 200 # Number of MCMC samples per burst
thin: 20 # Thin MCMC samples every `thin` iterations
num_adaptation_iterations: 1000
ThinPosterior: # Post-process further chain thinning HDF5 -> .pkl.
start: 3000
start: -10000
end:
by: 4
by: 10
Geopackage: # covid.tasks.summary_geopackage
base_geopackage: data/UK2019mod_pop.gpkg
base_layer: UK2019mod_pop_xgen
AWSS3:
profile: covid-pipeline
bucket: lancaster-covid-devel
S3:
profile: covid-pipeline-data
bucket: covid-pipeline-data
endpoint_url: https://fhm-chicas-storage.lancs.ac.uk
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