medium_term.yaml 1.42 KB
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# Covid_ODE model configuration

data:
  mobility_matrix: /home/jewellcp/Insync/jewellcp@lancaster.ac.uk/OneDrive Biz - Shared/covid19/data/UK_Commute_2019/mergedflows.csv
  population_size: /home/jewellcp/Insync/jewellcp@lancaster.ac.uk/OneDrive Biz - Shared/covid19/data/UK_Commute_2019/c2019modagepop.csv
  commute_volume: /home/jewellcp/Insync/jewellcp@lancaster.ac.uk/OneDrive Biz - Shared/covid19/data/DfT/2020-09-29/200929_OFF_SEN_COVID19_road_traffic_national_table.xlsx
  reported_cases: /home/jewellcp/Insync/jewellcp@lancaster.ac.uk/OneDrive Biz - Shared/covid19/data/PHE/PHE_2020-10-05/Anonymised Combined Line List 20201005.csv
  case_date_type: specimen
  pillar: '1'

parameter:
  beta1: 0.291   # R0 2.4
  beta2: 0.876   # Contact with commuters 1/3rd of the time
  beta3: 1.0   # lockdown vs normal
  omega: 1.0   # Non-linearity parameter for commuting volume
  nu: 0.5      # E -> I transition rate
  gamma: 0.45  # I -> R transition rate
  xi:
    - 2.07
    - 0.15
    - -1.08
    - -0.78
    - -0.73
    - -0.51

settings:
  inference_period:
    - 2020-07-12
    - 2020-10-02
  time_step: 1.
  prediction_period:
    - 2020-02-19
    - 2020-08-01

mcmc:
  dmax: 21
  nmax: 50
  m: 1
  occult_nmax: 5
  num_event_time_updates: 35
  num_bursts: 200
  num_burst_samples: 1000
  thin: 20
  
output:
  results_dir: 
  posterior: posterior.hd5
  national_rt: national_rt.xlsx
  medium_term: medium_term.xlsx
  geopackage: prediction.gpkg