cases_within_radius: Check Cases Within Radius

In certe-medical-epidemiology/certegis: A Certe R Package for Geographic Information Science

Check Cases Within Radius

Description

Based on the postcodes4_afstanden data set, this function determines the specified minimum number of cases within a certain radius.

Usage

cases_within_radius(
  data,
  radius_km = 10,
  minimum_cases = 10,
  column_count = NULL,
  ...
)

Arguments

data	data set containing a column 'postcode'
radius_km	radius in kilometres from each zip code. The search diameter is twice this number (since zip codes e.g. to the west and to the east are searched).
minimum_cases	minimum number of cases to search for
column_count	column name in data with the number of case counts, defaults to the first column with numeric values
...	ignored, allows for future extensions

Value

This function adds two columns ("cases_within_radius" ⁠<dbl>⁠ and "minimum_met" ⁠<lgl>⁠) to the input data.

Examples

library(dplyr, warn.conflicts = FALSE)

postcodes_friesland <- geo_postcodes4 |> 
  filter_geolocation(provincie == "Friesland") |> 
  pull(postcode)

# example with Norovirus cases:
noro <- data.frame(postcode = postcodes_friesland,
                   n = floor(runif(length(postcodes_friesland),
                                   min = 0, max = 3)))
head(noro)

radial_check <- cases_within_radius(noro, radius_km = 10, minimum_cases = 10)
head(radial_check)


# dplyr group support:
mdro <- data.frame(type = rep(c("ESBL", "MRSA", "VRE"), 20),
                   pc4 = postcodes_friesland[1:20],
                   n = floor(runif(60, min = 0, max = 3)))
mdro |> 
  group_by(type) |> 
  cases_within_radius()
  
  
# plotting support:
if (require("certeplot2")) {

  radial_check |>
    add_map() |>
    filter_geolocation(provincie == "Friesland") |>
    plot2(category = cases_within_radius,
          category.title = "Cases",
          datalabels = FALSE,
          colour_fill = "viridis")

}

certe-medical-epidemiology/certegis documentation built on Dec. 10, 2024, 6:27 a.m.