Generate multiple <daedalus_infection>s from parameter distributions — make_infection

Generate multiple <daedalus_infection>s from parameter distributions

Usage

make_infection_samples(
  name,
  param_distributions,
  param_ranges = NULL,
  samples = 100
)

Arguments

name: An infection name from among daedalus.data::epidemic_names.
param_distributions: A named list of <distribution> class objects provided by distributional, with names corresponding to daedalus.data::infection_parameter_names. These are used to generate samples draws from each distribution for the corresponding infection parameters. Arguments which vary by age are supported, with the drawn and scaled value treated as the median of the profile vector. See Examples.
param_ranges: An optional named list of two-element vectors, giving the ranges to which samples drawn using param_distributions should be rescaled. This allows easy rescaling of values drawn from bounded distributions (e.g. the Beta distribution). If passed, the list must have names corresponding to param_distribution names. When empty, the generated values are used without scaling. See Examples.
samples: The number of samples to generate.

Value

A list of <daedalus_infection> objects.

Examples

# make 10 infection objects varying in R0, with a skewed distribution
# scaled between 1.0 and 2.0
make_infection_samples(
  "influenza_2009",
  samples = 3,
  list(
    r0 = distributional::dist_beta(2, 5)
  ),
  list(
    r0 = c(0.1, 0.2)
  )
)
#> [[1]]
#> <daedalus_infection>
#> • Epidemic name: influenza_2009
#> • R0: 0.2
#> • sigma: 0.909
#> • p_sigma: 0.669
#> • epsilon: 0.58
#> • rho: 0.003
#> • eta: 0.003, 0.003, 0.001, and 0.006
#> • hfr: 0.04, 0.063, 0.041, and 0.634
#> • gamma_Ia: 0.4
#> • gamma_Is: 0.4
#> • gamma_H_recovery: 0.2
#> • gamma_H_death: 0.2
#> 
#> [[2]]
#> <daedalus_infection>
#> • Epidemic name: influenza_2009
#> • R0: 0.1
#> • sigma: 0.909
#> • p_sigma: 0.669
#> • epsilon: 0.58
#> • rho: 0.003
#> • eta: 0.003, 0.003, 0.001, and 0.006
#> • hfr: 0.04, 0.063, 0.041, and 0.634
#> • gamma_Ia: 0.4
#> • gamma_Is: 0.4
#> • gamma_H_recovery: 0.2
#> • gamma_H_death: 0.2
#> 
#> [[3]]
#> <daedalus_infection>
#> • Epidemic name: influenza_2009
#> • R0: 0.182723943621094
#> • sigma: 0.909
#> • p_sigma: 0.669
#> • epsilon: 0.58
#> • rho: 0.003
#> • eta: 0.003, 0.003, 0.001, and 0.006
#> • hfr: 0.04, 0.063, 0.041, and 0.634
#> • gamma_Ia: 0.4
#> • gamma_Is: 0.4
#> • gamma_H_recovery: 0.2
#> • gamma_H_death: 0.2
#>