spatial_project: Project future incidence

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

Project future incidence

Description

Simulate future incidence based on past incidence in multiple locations, a matrix of (possibly time-varying) reproduction numbers for each location, a matrix of serial intervals, a matrix of relative movement between locations.

Usage

spatial_project(x, R, si, pmovement, n_sim, n_days, model = "poisson")

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	A n_days X n_locations matrix of reproduction numbers; where n_days is either 1 or the number of days over which we want to project, and n_locations is the number of locations (i.e. the number of columns in x). If R has only 1 row, the values will be recycled.
si	A matrix of discretised serial interval, assumed to be the same same for all locations. These can be generated easily using the package EpiEstim. See vignettes for examples.
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.
n_sim	The number of epicurves to simulate. Defaults to 100.
n_days	projection horizon. Defaults to 7.
model	Currently only "poisson" is supported

Value

an array conatining the projected incidence. The dimensions of the returned array are n_days X n_locations X n_sim

Author(s)

Sangeeta Bhatia, Anne Cori, Pierre Nouvellet

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