force_of_infection: Force of infection under a spatially explicit brancing...

In mrc-ide/spatialbranchr: Spatially explicit branching process model

Force of infection under a spatially explicit brancing process model

Description

This function computes the force of infection at time t + 1 at locations 1, 2,....n given incidence (by onset) at these locations, the serial interval and the probabilities of movement of individuals during their infectious period.

Usage

force_of_infection(x, r_t, ws, pmovement)

Arguments

x	A matrix of past incidence (integer). The matrix has 1 column for each location; that is, each column is interpreted as the incidence in a location.
r_t	A matrix of reproduction numbers at times 1 through t in locations 1 through n.
ws	flipped serial interval
pmovement	A n_locations X n_locations matrix of the probability of movement between locations. Entry in row i, column j is the probability that a case in i will move to j during their infectious period.

Value

vector; overall force of infection at each location.

Author(s)

Sangeeta Bhatia, Anne Cori, Pierre Nouvellet

mrc-ide/spatialbranchr documentation built on Oct. 2, 2022, 5:56 p.m.