dist_fit: Fit an Integer Adjusted Exponential, Gamma or Lognormal...

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

Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions

Description

Fits an integer adjusted exponential, gamma or lognormal distribution using stan.

Usage

dist_fit(
  values = NULL,
  samples = 1000,
  cores = 1,
  chains = 2,
  dist = "exp",
  verbose = FALSE,
  backend = "rstan"
)

Arguments

values	Numeric vector of values
samples	Numeric, number of samples to take. Must be >= 1000. Defaults to 1000.
cores	Numeric, defaults to 1. Number of CPU cores to use (no effect if greater than the number of chains).
chains	Numeric, defaults to 2. Number of MCMC chains to use. More is better with the minimum being two.
dist	Character string, which distribution to fit. Defaults to exponential ("exp") but gamma ("gamma") and lognormal ("lognormal") are also supported.
verbose	Logical, defaults to FALSE. Should verbose progress messages be printed.
backend	Character string indicating the backend to use for fitting stan models. Supported arguments are "rstan" (default) or "cmdstanr".

Value

A stan fit of an interval censored distribution

Examples

# integer adjusted exponential model
dist_fit(rexp(1:100, 2),
  samples = 1000, dist = "exp",
  cores = ifelse(interactive(), 4, 1), verbose = TRUE
)


# integer adjusted gamma model
dist_fit(rgamma(1:100, 5, 5),
  samples = 1000, dist = "gamma",
  cores = ifelse(interactive(), 4, 1), verbose = TRUE
)

# integer adjusted lognormal model
dist_fit(rlnorm(1:100, log(5), 0.2),
  samples = 1000, dist = "lognormal",
  cores = ifelse(interactive(), 4, 1), verbose = TRUE
)

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