process_spatial_estimate: Process the spatially explicit branching process model fitted...

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

Process the spatially explicit branching process model fitted to incidence

Description

This function processes the fitted object returned by 'spatial_estimate'. The processing consists of translating the vector of effective reproduction number parameters to a space-time matrix that is easier to interpret.

Usage

process_spatial_estimate(fit, x, window, samples = 1000L)

Arguments

fit	stanfit object returned by 'spatial_estimate'
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.
window	integer indicating the length of the window over which Rt is to be estimated. Window length is assumed to be the same for all locations. Default value is 7 i.e. Rt is estimated over a weekly window. Currently only non-overlapping windows are supported.
samples	a non-negative integer giving the desired number of samples from the posterior distribution of each parameter.

Value

a list with the 3 elements: (1) a three-dimensional matrix where the first dimension is time, the second dimension is the number of spatial units, and the thirs dimesnion is the desired number of samples from the posterior distributions of Rt; (2)

Author(s)

Sangeeta Bhatia

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