swash (version 1.2.1)

R_t: Effective Reproduction Number for Epidemic Data

Description

Calculation of the effective reproduction number for infection/surveillance data

Usage

R_t(
  infections, 
  GP = 4,
  correction = FALSE
  )

Value

list with two entries:

R_t:

Object of class "numeric" \(R_t\) values

infections_data:

Object of class "data.frame" Dataset with infections data and \(R_t\)

Arguments

infections

numeric vector with infection data

GP

Generation period, in days

correction

Correction of values equal to zero? (Recommended)

Author

Thomas Wieland

Details

The function calculates the effective reproduction number (=growth factor), \(R_t\), of an infections time series.

References

Bonifazi G et al. (2021) A simplified estimate of the effective reproduction number Rt using its relation with the doubling time and application to Italian COVID-19 data. The European Physical Journal Plus 136, 386. tools:::Rd_expr_doi("https://doi.org/10.1140/epjp/s13360-021-01339-6")

Wieland T (2020) A phenomenological approach to assessing the effectiveness of COVID-19 related nonpharmaceutical interventions in Germany. Safety Science 131, 104924. tools:::Rd_expr_doi("https://doi.org/10.1016/j.ssci.2020.104924")

See Also

logistic_growth

Examples

data(COVID19Cases_geoRegion)
# Get SWISS COVID19 cases at NUTS 3 level

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[!COVID19Cases_geoRegion$geoRegion %in% c("CH", "CHFL"),]
# Exclude CH = Switzerland total and CHFL = Switzerland and Liechtenstein total

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[COVID19Cases_geoRegion$datum <= "2020-05-31",]
# Extract first COVID-19 wave

COVID19Cases_BS <-
  COVID19Cases_geoRegion[(COVID19Cases_geoRegion$geoRegion == "ZH")
                         & (COVID19Cases_geoRegion$sumTotal > 0),]
# COVID cases for Zurich

Rt_BS <- R_t(infections = COVID19Cases_BS$entries)
# Effective reproduction number

Rt_BS