template_config.yaml 1.05 KB
Newer Older
Chris Jewell's avatar
Chris Jewell committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
# Covid_ODE model configuration

data:
  mobility_matrix: data/mergedflows.csv
  population_size: data/c2019modagepop.csv
  commute_volume: data/200929_OFF_SEN_COVID19_road_traffic_national_table.xlsx
  reported_cases: data/Anonymised Combined Line List 20201002.csv
  case_date_type: specimen
  pillar: both

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:
    - 2020-07-03
    - 2020-09-29
  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: $global_scratch/covid19/
  posterior: posterior.hd5
  national_rt: national_rt.xlsx
  geopackage: prediction.gpkg