Rates and Ratios — attack

Calculate attack rate, case fatality rate, and mortality rate

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
#>   cases population ar lower upper
#> 1    10         50 20 11.24 33.04

# print them inline using `fmt_ci_df()`
fmt_ci_df(ar)
#> [1] "20.00% (CI 11.24--33.04)"

# Alternatively, if you want one column for the CI, use `mergeCI = TRUE`
attack_rate(10, 50, mergeCI = TRUE, digits = 2) # 20% attack rate
#>   cases population ar             ci
#> 1    10         50 20 (11.24--33.04)

print(cfr <- case_fatality_rate(1, 100), digits = 2) # CFR of 1%
#>   deaths population cfr lower upper
#> 1      1        100   1  0.18   5.4
fmt_ci_df(cfr)
#> [1] "1.00% (CI 0.18--5.45)"

# using a data frame
if (require("outbreaks")) {
  withAutoprint({
  e <- outbreaks::ebola_sim$linelist
  case_fatality_rate_df(e,
    outcome == "Death",
    group = gender,
    add_total = TRUE,
    mergeCI = TRUE
  )
  })
}
#> Loading required package: outbreaks
#> > e <- outbreaks::ebola_sim$linelist
#> > case_fatality_rate_df(e, outcome == "Death", group = gender, add_total = TRUE, 
#> +     mergeCI = TRUE)
#> # A tibble: 3 × 5
#>   gender deaths population   cfr ci            
#>   <fct>   <int>      <int> <dbl> <chr>         
#> 1 f        1301       2299  56.6 (54.55--58.60)
#> 2 m        1281       2266  56.5 (54.48--58.56)
#> 3 Total    2582       4565  56.6 (55.12--57.99)