WhiteLabRt (version 1.0.1)

spatialRt: Run Spatial R(t) estimation and Estimate Reproduction Numbers

Description

This function calculates R(t) that arises from transfer of infectors between different states. There are different flavors of the model, but the base version calculates a weekly R(t) within each state.

Usage

spatialRt(report_dates, case_matrix, transfer_matrix, sip, v2 = FALSE, ...)

Value

An rstan object.

Arguments

report_dates

A vector of reporting dates

case_matrix

A matrix of cases, defined by integers

transfer_matrix

A matrix that defines how infectors flow between states. Each row of the transfer matrix must sum to 1.

sip

Vector of numeric values specifying the serial interval probabilities.

v2

a flag indicating FALSE if the base algorithm is to be used, and TRUE if the experimental algorithm is desired. The experimental version contains a non-centered parameterization, an AR1 process, and partial pooling across states.

...

Additional arguments passed to rstan::sampling()

Examples

# \donttest{
data("sample_multi_site")
data("transfer_matrix")
Y <- matrix(integer(1), nrow = nrow(sample_multi_site), ncol = 2)
for(i in 1:nrow(Y)) {
  for(j in c(2, 3)) {
    Y[i,j-1] <- as.integer(sample_multi_site[i,j])
  }
}
all(is.integer(Y))
sip <- si(14, 4.29, 1.18, leading0 = FALSE)
sample_m_hier <- spatialRt(report_dates = sample_multi_site$date,
case_matrix = Y,
transfer_matrix = transfer_matrix,
v2 = FALSE,
sip = sip, chains = 1)
# }