plot_map: Map Plot of Specified Indicator

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

Map Plot of Specified Indicator

Description

Plot of a map showing a speficied indicator (such as incidence) from an infpan object.

Usage

plot_map(
    object,
    attribute = "Cases",
    timepoint = NULL,
    verbose = FALSE,
    ...
  )

Arguments

object	object of class infpan
attribute	Attribute to be plotted, must be defined in infpan object (e.g., "Cases", "Incidence")
timepoint	Time point for which the attribute is to be plotted
verbose	bool argument which indicates whether progress messages are displayed
...	Further graphic arguments passed to sf::plot, e.g. breaks, colors

Details

Plots a map from an infpan object which displays the attribute specified with the attribute parameter at the timepoint specified with timepoint. To adjust the layout of the map, use the ... parameters which are passed to the plot S3 method for the sf class (see the corresponding documentation). Map plot requires geodata to be specified in the infpan object (Use add_geodata to assign your sf object). Permitted attributes are: "Cases", "R_t" (Effective reproduction number), "Cum. cases" (Cumulative cases), "Incidence" Incidence (per xxx pop), "Population" (Population size of the region), "Roll. mean" (Rolling mean of cases), and "Roll. sum" (Rolling sum of cases).

Value

Input infpan object (unchanged), plot

Author(s)

Thomas Wieland

References

Wieland T (2020) Flatten the Curve! Modeling SARS-CoV-2/COVID-19 Growth in Germany at the County Level. REGION 7(2), 43–83. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.18335/region.v7i2.324")}

See Also

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

Examples

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

data(K4kant20260101gf_ch2007Poly)
# Cantonal boundaries of Switzerland

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_incidence(
  infpan_CH, 
  col_name = "incidence",
  verbose = TRUE
)
# Calculate incidence of cases as "incidence"

infpan_CH <- add_geodata(
  infpan_CH,
  K4kant20260101gf_ch2007Poly,
  unit_col = "cant_abbrev"
)
# Adding geodata (sf) to infpan object

summary(infpan_CH)
# Summary of infpan object

timestamps(infpan_CH)
# Time stamps of infpan object

plot_map(
  infpan_CH,
  attribute = "Incidence",
  main = "COVID-19 Incidence 2020-05-31",
  breaks = c(0, 0.05, 0.1, 0.2, 1),
  verbose = TRUE
)
# Simple map of incidence for the most current date (timepoint=NULL)

swash documentation built on Oct. 18, 2026, 5:06 p.m.