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.
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). IfRhas 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