bootstrapped_dist_fit: Fit a Subsampled Bootstrap to Integer Values and Summarise...

In epiforecasts/EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters

Description

Fits an integer adjusted distribution to a subsampled bootstrap of data and then integrates the posterior samples into a single set of summary statistics. Can be used to generate a robust reporting delay that accounts for the fact the underlying delay likely varies over time or that the size of the available reporting delay sample may not be representative of the current case load.

Usage

bootstrapped_dist_fit(
  values,
  dist = "lognormal",
  samples = 2000,
  bootstraps = 10,
  bootstrap_samples = 250,
  max_value,
  verbose = FALSE
)

Arguments

values	Integer vector of values.
dist	Character string, which distribution to fit. Defaults to lognormal ("lognormal") but gamma ("gamma") is also supported.
samples	Numeric, number of samples to take overall from the bootstrapped posteriors.
bootstraps	Numeric, defaults to 1. The number of bootstrap samples (with replacement) of the delay distribution to take. If samples is less than bootstraps, samples takes the value of bootstraps.
bootstrap_samples	Numeric, defaults to 250. The number of samples to take in each bootstrap if the sample size of the supplied delay distribution is less than its value.
max_value	Numeric, defaults to the maximum value in the observed data. Maximum delay to allow (added to output but does impact fitting).
verbose	Logical, defaults to FALSE. Should progress messages be printed.

Value

A ⁠<dist_spec>⁠ object summarising the bootstrapped distribution

Examples

# lognormal
delays <- rlnorm(500, log(5), 1)
out <- bootstrapped_dist_fit(delays,
  samples = 1000, bootstraps = 10,
  dist = "lognormal"
)
out

epiforecasts/EpiNow2 documentation built on Dec. 10, 2024, 5:32 p.m.