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Calculate Active/Passive IFR/SIR From True IFR/SIR And Detection Rates

Source: R/calculate_observed_ifr_sir.R
calculate_observed_ifr_sir.Rd

Calculate Active/Passive IFR/SIR From True IFR/SIR And Detection Rates

Usage

calculate_observed_ifr_sir(
  strata,
  passive_asymptomatic_detection,
  passive_symptomatic_detection
)

Arguments

strata

A data.frame like object with the columns 'population', 'sir', and 'ifr'. Any additional columns are treated as descriptions for the strata. If strata only contains the columns 'population', 'sir', 'ifr' it's assumed that the sample data set contains no strata.

passive_asymptomatic_detection

The probability of detecting a case presenting asymptomatically through passive surveillance.

passive_symptomatic_detection

The probability of detecting a case presenting symptomatically through passive surveillance.

Value

The given strata data.frame with the additional columns 'theta', 'active_sir', 'passive_sir', 'active_ifr', and 'passive_ifr'.

Examples

strata <- data.frame(
  population = 1000L,
  sir = 0.15,
  ifr = 0.02
)
calculate_observed_ifr_sir(
  strata,
  passive_asymptomatic_detection = 0.2,
  passive_symptomatic_detection = 0.6
)
#>   population  sir  ifr theta active_sir passive_sir active_ifr passive_ifr
#> 1       1000 0.15 0.02  0.26       0.15   0.3937409       0.02   0.0727802