template_config.yaml 1.19 KB
Newer Older
Chris Jewell's avatar
Chris Jewell committed
1
2
3
4
5
# Covid_ODE model configuration

data:
  mobility_matrix: data/mergedflows.csv
  population_size: data/c2019modagepop.csv
6
  commute_volume: data/201204_OFF_SEN_COVID19_road_traffic_national_table.xlsx
Chris Jewell's avatar
Chris Jewell committed
7
  reported_cases: data/Anonymised Combined Line List 20201109.csv
Chris Jewell's avatar
Chris Jewell committed
8
9
  case_date_type: specimen
  pillar: both
10
  tier_restriction_csv: data/tidyLAD19Tiers.csv
Chris Jewell's avatar
Chris Jewell committed
11
  geopackage: data/UK2019mod_pop.gpkg
Chris Jewell's avatar
Chris Jewell committed
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

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:
38
  dmax: 84
Chris Jewell's avatar
Chris Jewell committed
39
40
  nmax: 50
  m: 1
Chris Jewell's avatar
Chris Jewell committed
41
  occult_nmax: 15
Chris Jewell's avatar
Chris Jewell committed
42
43
  num_event_time_updates: 35
  num_bursts: 200
Chris Jewell's avatar
Chris Jewell committed
44
  num_burst_samples: 50
Chris Jewell's avatar
Chris Jewell committed
45
  thin: 20
46
47
48
49
50
  prior:
    gamma:
      concentration: 2.0
      rate: 4.0

Chris Jewell's avatar
Chris Jewell committed
51
52
53
54
55
output:
  results_dir: $global_scratch/covid19/
  posterior: posterior.hd5
  national_rt: national_rt.xlsx
  geopackage: prediction.gpkg