attack_rate: Rates and Ratios

In epikit: Miscellaneous Helper Tools for Epidemiologists

Rates and Ratios

Description

Calculate attack rate, case fatality rate, and mortality rate

Usage

attack_rate(
  cases,
  population,
  conf_level = 0.95,
  multiplier = 100,
  mergeCI = FALSE,
  digits = 2
)

case_fatality_rate(
  deaths,
  population,
  conf_level = 0.95,
  multiplier = 100,
  mergeCI = FALSE,
  digits = 2
)

case_fatality_rate_df(
  x,
  deaths,
  group = NULL,
  conf_level = 0.95,
  multiplier = 100,
  mergeCI = FALSE,
  digits = 2,
  add_total = FALSE
)

mortality_rate(
  deaths,
  population,
  conf_level = 0.95,
  multiplier = 10^4,
  mergeCI = FALSE,
  digits = 2
)

Arguments

cases, deaths	number of cases or deaths in a population. For _df functions, this can be the name of a logical column OR an evaluated logical expression (see examples).
population	the number of individuals in the population.
conf_level	a number representing the confidence level for which to calculate the confidence interval. Defaults to 0.95, representing a 95% confidence interval using binom::binom.wilson()
multiplier	The base by which to multiply the output: multiplier = 1: ratio between 0 and 1 multiplier = 100: proportion multiplier = 10^4: x per 10,000 people
mergeCI	Whether or not to put the confidence intervals in one column (default is FALSE)
digits	if mergeCI = TRUE, this determines how many digits are printed
x	a data frame
group	the bare name of a column to use for stratifying the output
add_total	if group is not NULL, then this will add a row containing the total value across all groups.

Value

a data frame with five columns that represent the numerator, denominator, rate, lower bound, and upper bound.

• attack_rate(): cases, population, ar, lower, upper

• case_fatality_rate(): deaths, population, cfr, lower, upper

Examples

# Attack rates can be calculated with just two numbers
print(ar <- attack_rate(10, 50), digits = 4) # 20% attack rate

# print them inline using `fmt_ci_df()`
fmt_ci_df(ar)

# Alternatively, if you want one column for the CI, use `mergeCI = TRUE`
attack_rate(10, 50, mergeCI = TRUE, digits = 2) # 20% attack rate

print(cfr <- case_fatality_rate(1, 100), digits = 2) # CFR of 1%
fmt_ci_df(cfr)

# using a data frame
if (require("outbreaks")) {
  withAutoprint({
  e <- outbreaks::ebola_sim$linelist
  case_fatality_rate_df(e,
    outcome == "Death",
    group = gender,
    add_total = TRUE,
    mergeCI = TRUE
  )
  })
}

epikit documentation built on Feb. 16, 2023, 7:42 p.m.