spread (version 2019.8.5)

commuter: commuter

Description

This model is a stochastic SEIIaR (susceptible, exposed, infectious, infectious asymptomatic, recovered) metapopulation model that including commuting.

Usage

commuter(seiiar = spread::norway_seiiar_oslo_2017,
  commuters = spread::norway_commuters_2017, r0 = NULL, beta = NULL,
  latent_period = 1.9, infectious_period = 3, asymptomatic_prob = 0,
  asymptomatic_relative_infectiousness = 0, days_simulation = 7 * 8,
  N = 1)

Arguments

seiiar

Data frame containing `location_code`, `S`, `E`, `I`, `Ia`, and `R` for the entire population

commuters

Data frame comtaining `from`, `to`, `n` for the number of people who travel

r0

Float, basic reproduction number

beta

Float, infection parameter, 0.6

latent_period

Float, 1.9

infectious_period

Float, 3

asymptomatic_prob

Float, Proportion/probability of asymptomatic given infectious

asymptomatic_relative_infectiousness

Float, Relative infectiousness of asymptomatic infectious

days_simulation

Int, Number of days to simulate

N

Int = 1 int, Number of repetitions

Details

Each location has a local infection system, while the locations are connected by people who commute each day. The model differentiates between day and night. During the day you can infect/be infected in the location where you work, while during the night you can infect/be infected in the location where you live. It is the same commuters who travel back and forth each day. At the start of a day, all commuters are sent to their work location, where they mix for 12 hours. The commuters are then sent to their respective home locations, where they mix for 12 hours.

The model is loosely based upon a published model by Engebretsen (2019) 10.1371/journal.pcbi.1006879.

For more information, look at vignette("commuter_model","spread")

Examples

# NOT RUN {
spread::commuter(
  seiiar = spread::norway_seiiar_measles_oslo_2017,
  commuters = spread::norway_commuters_2017,
  r0 = 14,
  latent_period = 8,
  infectious_period = 5,
  asymptomatic_prob = 0,
  asymptomatic_relative_infectiousness = 0,
  days_simulation = 7*9,
  N = 1
)
# }