Simulation of Ireland

[mghosh00]

Is your feature request related to a problem? Please describe. We wish to simulate the population of Ireland, as there is good spatial heterogeneity and the country has a reasonable population size (~5 million).

Describe the solution you'd like

• Retrieve geographical parameters from EpiGeoPop
• Modify any other parameters necessary (e.g. household parameters)

Additional context This data will be used across EpiOS stratified sampling, branching processes and SEIR inference

[mghosh00]

Parameters

We will tick off the parameters from Ireland when we get them. Here are a list of parameters from the .json files:

Hyperparameters

• [x] basic_reproduction_num
• [x] mcell_num_per_cell
• [x] ave_places_per_mcell
• [x] infection_radius
• [x] time_steps_per_day

Disease parameters

• [x] latent_period
• [x] asympt_infect_period
• [x] mean_x_to_y (10 params)
• [x] x_icdf (12 lists)
• [x] CDF_RES
• [x] prob_symptomatic
• [x] sympt_infectiousness
• [x] asympt_infectiousness
• [x] infectiousness_prof
• [x] latent_to_sympt_delay
• [x] max_infectious_steps
• [x] inf_prof_res
• [x] host_progression_lists

Place parameters

• [ ] place_params - age_group_props
• [x] place_transmission
• [x] carehome_params

Household parameters

• [x] household_transmission
• [x] household_size_distribution
• [x] max_household_size
• [x] household_age_params

Age parameters

• [x] use_ages
• [x] age_proportions
• [x] age_contact

Waning immunity parameters

• [x] use_waning_immunity
• [x] rate_multiplier_params
• [x] antibody_level_params

[mghosh00]

Input

We also need an input.csv file (see gib_input.csv), hopefully this is produced by EpiGeoPop

[abbie-evans]

Household_size_distribution: [0.08518602, 0.20812382, 0.19097004, 0.24683137, 0.16569818, 0.06929404, 0.00847413, 0.00847413, 0.00847413, 0.00847412]

Values calculated from: https://data.cso.ie/ https://data.cso.ie/table/TAH02