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Compute average incidence over a set day interval

Source: R/helpers.R
calc_window_incidence.Rd

Compute average incidence over a set day interval

Usage

calc_window_incidence(data, type = c("cases", "deaths"), window = 14)

Arguments

data

a data.frame with required columns to compute the metric

type

(character) one of cases or deaths, specifying the appropriate basis for the metric

window

(numeric, default: 14) a numeric representing days to calculate the metric over

Value

a data.frame of summarized incidence values (ave_incidence) by date, possibly including grouping vars if data were grouped.

Details

For type == "cases", data should contain at least date, new_cases, and population columns. For type == "deaths", data should contain new_deaths instead.

Note that incidence here is per 100K population. The function assumes that data passed has observations for each day for each country, since we use and index-based approach to compute average incidence, not calendar-time.

Examples

if (FALSE) {
data <- get_covid_df("WHO")
# 14d average incidence world-wide
calc_window_incidence(window = 14)
# For grouped operations, group data beforehand and pipe:
# 14d average incidence by country
data |>
  group_by(iso2code, country) |>
  calc_window_incidence(window = 14)
}