swash_backwash: Swash-Backwash Model for the Single Epidemic Wave

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

Swash-Backwash Model for the Single Epidemic Wave

Description

Analysis of regional infection/surveillance data using the Swash-Backwash Model for the Single Epidemic Wave by Cliff and Haggett (2006).

Usage

swash_backwash(
  infpan = NULL,
  data = NULL,
  col_cases = NULL, 
  col_date = NULL, 
  col_region = NULL,
  time_format = "%Y-%m-%d",
  verbose = FALSE
  )

Arguments

infpan	infpan object containing regional infection data
data	data.frame with regional infection data
col_cases	Column containing the cases (numeric)
col_date	Column containing the time points (e.g., days)
col_region	Column containing the unique identifier of the regions (e.g., name, NUTS 3 code)
time_format	character, Time format of the values in col_date
verbose	bool argument which indicates whether progress messages are displayed

Details

The function performs the analysis of the input panel data with N regions and T time points using the Swash-Backwash Model. The user must state panel data with daily infections.

The Swash-Backwash Model (SBM) for the Single Epidemic Wave is the spatial equivalent of the classic epidemiological SIR (Susceptible-Infected-Recovered) model. It was developed by Cliff and Haggett (2006) to model the velocity of spread of infectious diseases across space. Current applications can be found, for example, in Smallman-Raynor et al. (2022a,b). The function swash_backwash() enables the calculation of the Swash-Backwash Model for user-supplied panel data on regional infections. It calculates the model and creates a model object of the sbm class defined in this package. This class can be used to visualize results (summary(), plot()) and calculate bootstrap confidence intervals for the model estimates (confint(sbm)); the latter returns an object of class sbm_ci as defined in this package. Two sbm_ci objects for different countries may be compared with compare_countries(), which allows the estimation of mean differences of a user-specified model parameter (e.g., spatial reproduction number R_{OA}) between two countries. This makes it possible to check whether the spatial spread velocity of a communicable disease is significantly different in one country than in another country; the result is an object of class countries.

To calculate the SBM model based on an infpan object, use the corresponding method swash(infpan).

Value

object of class sbm-class

Author(s)

Thomas Wieland

References

Cliff AD, Haggett P (2006) A swash-backwash model of the single epidemic wave. Journal of Geographical Systems 8(3), 227-252. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s10109-006-0027-8")}

Smallman-Raynor MR, Cliff AD, Stickler PJ (2022) Meningococcal Meningitis and Coal Mining in Provincial England: Geographical Perspectives on a Major Epidemic, 1929–33. Geographical Analysis 54, 197–216. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1111/gean.12272")}

Smallman-Raynor MR, Cliff AD, The COVID-19 Genomics UK (COG-UK) Consortium (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection 150, e145. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1017/S0950268822001285")}.

See Also

sbm-class, swash

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

CH_covidwave1 <- 
  swash_backwash(
    data = COVID19Cases_geoRegion, 
    col_cases = "entries", 
    col_date = "datum", 
    col_region = "geoRegion"
    )
# Swash-Backwash Model for Swiss COVID19 cases
# Spatial aggregate: NUTS 3 (cantons)

summary(CH_covidwave1)
# Summary of Swash-Backwash Model

plot(CH_covidwave1)
# Plot of Swash-Backwash Model edges and total epidemic curve

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