R_t: Effective Reproduction Number for Epidemic Data
In swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Data

R_t	R Documentation

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
  )

Arguments

`infections`	`numeric vector` with infection data
`GP`	Generation period, in time units (typically days)
`correction`	Correction of values equal to zero? (Recommended)

Details

The function calculates the effective reproduction number, R_t, of an infections time series. Set the generation period by the parameter GP (default: 4). If correction is TRUE, values equal to zero are increased by one.

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`

Author(s)

Thomas Wieland

References

an der Heiden M, Hamouda O (2020) Schätzung der aktuellen Entwicklung der SARS-CoV-2-Epidemie in Deutschland - Nowcasting. Epidemiologisches Bulletin 17, 10-15. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.25646/6692")}

Bonifazi G, Lista L, Menasce D, Mezzetto M, Pedrini D, Spighi R, Zoccoli A (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. \Sexpr[results=rd]{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. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1016/j.ssci.2020.104924")}

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

swash documentation built on April 7, 2026, 1:06 a.m.