calculate_rollmean: Rolling Means of Infection Numbers

In swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Data

Rolling Means of Infection Numbers

Description

Calculation of the rolling means of infection numbers for infections panel data.

Usage

calculate_rollmean(
  object,
  k = 7,
  align = "center",
  fill = NA,
  col_name = NULL,
  overwrite = FALSE,
  verbose = FALSE
  )

Arguments

object	object of class infpan
k	integer width of the rolling window (default: 7)
align	character specifying whether the rolling mean should be left- or right-aligned or centered (default) compared to the rolling window (default: center)
fill	numeric value or NA for the filling value at the left/within/right end of the data range
col_name	character value specifying the column name of the computed rolling means
overwrite	bool argument which indicates whether the column should be overwritten if already existing
verbose	bool argument which indicates whether progress messages are displayed

Details

Calculates the rolling mean of the infections panel data for all time points for each region. Set the rolling window by the parameter k (default: 7). Set the fill value for the observations left/within/right to the data range with parameter fill (default: NA). Parameter align defines whether the index of the result should be left- or right-aligned or centered (default). If col_name is NULL, the column is defined as "<Column name of cases>_rm". Set overwrite to TRUE, if an existing column should be overwritten. The method uses the function rollmean from the zoo package (see the corresponding documentation).

Value

infpan object including column with rolling means in the infections panel data

Author(s)

Thomas Wieland

References

Wieland T (2025) Assessing the effectiveness of non-pharmaceutical interventions in the SARS-CoV-2 pandemic: results of a natural experiment regarding Baden-Württemberg (Germany) and Switzerland in the second infection wave. Journal of Public Health 33(11), 2497-2511. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s10389-024-02218-x")}

See Also

infpan-class, load_infections_paneldata, calculate_rollsum, calculate_Rt, calculate_cum, calculate_incidence

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

infpan_CH <- load_infections_paneldata(
    data = COVID19Cases_geoRegion,
    col_cases = "entries",
    col_date = "datum",
    col_region = "geoRegion",
    other_cols = c("Population" = "pop"), 
    verbose = TRUE
  )
# Import as infections panel data set (class infpan)

infpan_CH <- calculate_rollmean(
  infpan_CH, 
  col_name = "RollingMean",
  verbose = TRUE
)
# Calculate rolling mean of cases as "RollingMean"

summary(infpan_CH)
# Summary of infpan object

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