commuter: commuter

In spread: Infectious Disease Spread Models

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) doi: 10.1371/journal.pcbi.1006879.

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

Examples

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
)

Example output

PACKAGE: spread
Version: 2019.08.05 at 10:32
Commuter model and C++ code developed by Solveig Engebretsen and Andreas Nygård Osnes
Ported to RCPP by Richard White
Starting to add edges, printing every 1000 edge
1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 13000 14000 15000 16000 17000 18000 19000 20000 21000 22000 23000 24000 25000 26000 27000 28000 Found 28923 edges
Running 1 simulations of 63 days

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Finished all simulations

spread documentation built on Aug. 20, 2019, 5:13 p.m.