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Calculate Hazard Statistics

Source: R/calculate_hazard.R
calculate_hazard.Rd

Calculate a data.frame of posterior infection-hazard estimates broken down by time period and strata.

Usage

calculate_hazard(x, ...)

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

# S3 method for class 'list'
calculate_hazard(
  x,
  time_period,
  strata,
  population = NULL,
  mean_estimate = TRUE,
  median_estimate = TRUE,
  alpha = 0.05,
  ...
)

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

Arguments

x

An object to calculate hazard 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 hazard should be included in the mean_estimate column of the returned data.frame.

median_estimate

A single logical indicating if the median estimate for the hazard should be included in the median_estimate column of the returned data.frame.

alpha

A numeric of significance levels to return the hazard confidence intervals for. The columns will be in \{lower/upper\}_\{alpha\} format (i.e. lower_05 and upper_05 for alpha=0.05).

time_period

A data.frame describing the time-period dimension of the underlying hazard.

strata

A data.frame describing the strata dimension of the underlying hazard.

population

Optional numeric vector describing the population for each strata row. If provided, strata with zero population are excluded from the returned hazard summary.

Value

calculate_hazard.SeverityEstimateFit returns a data.frame describing posterior hazard estimates by time period and strata.

calculate_hazard.default signals an error.

Examples

logit_hzd <- array(
  qlogis(seq(0.01, 0.08, length.out = 8L)),
  dim = c(2L, 2L, 2L)
)
calculate_hazard(
  list(logit_hzd = logit_hzd),
  time_period = data.frame(week = 1L:2L),
  strata = data.frame(age = c("Adult", "Senior")),
  alpha = numeric()
)
#>   week    age mean_estimate median_estimate
#> 1    1  Adult         0.015           0.015
#> 2    1 Senior         0.055           0.055
#> 3    2  Adult         0.035           0.035
#> 4    2 Senior         0.075           0.075