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Calculate Fatality Ratio Statistics

Source: R/calculate_fatality_ratio.R
calculate_fatality_ratio.Rd

Calculate a data.frame of fatality ratios broken down by strata, as well as other optional model metrics.

Usage

calculate_fatality_ratio(x, ...)

# S3 method for class 'SeverityEstimateFit'
calculate_fatality_ratio(
  x,
  mean_estimate = TRUE,
  median_estimate = TRUE,
  naive_estimate = FALSE,
  alpha = 0.05,
  ...
)

# S3 method for class 'list'
calculate_fatality_ratio(
  x,
  strata,
  mean_estimate = TRUE,
  median_estimate = TRUE,
  naive_estimate = FALSE,
  alpha = 0.05,
  incidence = NULL,
  outcome = NULL,
  ...
)

# Default S3 method
calculate_fatality_ratio(x, ...)

Arguments

x

A object to calculate fatality ratio statistics from, typically a SeverityEstimateFit S4 object.

...

Further arguments passed to other methods.

mean_estimate

A single logical indicating if the mean estimate for the ratios should be included in the '*_mean_estimate' columns of the returned data.frame.

median_estimate

A single logical indicating if the median estimate for the ratios should be included in the '*_median_estimate column of the returned data.frame.

naive_estimate

A single logical indicating if the naive estimate for fatality ratio should be included in the 'naive_estimate' column.

alpha

A numeric of significance levels to return the parameters confidence intervals for. The columns will be in '*_{lower/upper}_{alpha}' format (i.e. '*_lower_05' and '*_upper_05' for alpha=0.05).

strata

A data.frame describing the strata rows to report. For the list method, these rows are used as the reference strata for the returned estimates.

incidence

An optional incidence array used to calculate naive fatality ratio estimates. This is required when naive_estimate = TRUE.

outcome

An optional outcome data.frame used to map the incidence array columns when calculating naive fatality ratio estimates. This is required when naive_estimate = TRUE.

Value

calculate_fatality_ratio.SeverityEstimateFit returns a data.frame describing fatality ratios by strata or, if no strata were provided when fitting a single row data.frame.

calculate_fatality_ratio.default signals an error.

Examples

draws <- list(
  C = matrix(1, nrow = 4L, ncol = 2L),
  mortality = matrix(c(0.01, 0.02, 0.03, 0.04, 0.02, 0.03, 0.04, 0.05),
    nrow = 4L
  ),
  xi = matrix(c(0.08, 0.10, 0.12, 0.14, 0.18, 0.20, 0.22, 0.24),
    nrow = 4L
  )
)
strata <- data.frame(age = c("Adult", "Senior"))
calculate_fatality_ratio(draws, strata = strata, alpha = numeric())
#>      age ifr_mean_estimate ifr_median_estimate sir_mean_estimate
#> 1  Adult             0.025               0.025              0.11
#> 2 Senior             0.035               0.035              0.21
#>   sir_median_estimate
#> 1                0.11
#> 2                0.21