Estimate the time-varying reproduction number from incidence data using covariate data

Estimate the time-varying reproduction number from incidence data using covariate data

Usage

fit_epifilter_covariates(N, C, w, X, is_sampling = TRUE, ...)

Arguments

N

number of data points

C

case counts

w

discretised serial interval

X

matrix of covariates (which likely should include a first column of 1s) of dimensions N x (N_covariates + 1)

is_sampling

Boolean indicating if sampling is to be used (if TRUE) or optimisation (if FALSE). Defaults to TRUE

...

Arguments passed to rstan::sampling() (if is_sampling=TRUE) or rstan::optimizing() (if is_sampling=FALSE)

Value

a stanfit object