lna_control: Generates a list of settings for sampling the latent LNA...

In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

Generates a list of settings for sampling the latent LNA paths and time-varying parameters via elliptical slice sampling.

Description

Generates a list of settings for sampling the latent LNA paths and time-varying parameters via elliptical slice sampling.

Usage

lna_control(
  n_updates = 1,
  bracket_width = 2 * pi,
  bracket_update_iter = Inf,
  bracket_scaling = 2 * sqrt(2 * log(10)),
  joint_strata_update = FALSE,
  joint_initdist_update = TRUE,
  approx_warmup = 100
)

Arguments

n_updates	number of elliptical slice sampling updates per MCMC iteration, defaults to 1.
bracket_width	width of the elliptical slice sampling bracket, must be in (0,2*pi], and default to 2*pi.
bracket_update_iter	iteration at which the widths of the elliptical slice sampling brackets should be shrunk, defaults to Inf and the bracket widths are kept constant.
bracket_scaling	Scaling factors for elliptical slice sampling bracket widths. If brackets are to be shrunk, the new width is set to the minimum of 2*pi or the scaling multiplied by the standard deviation of the previous ESS angles. The scalings default to the full width at one tenth maximum for a gaussian.
joint_strata_update	should all strata be updated jointly? Defaults to FALSE.
joint_initdist_update	should the initial states be updated jointly with the lna path? Defaults to TRUE, in which case initial conditions for each stratum are still paired with the LNA path for that stratum.
approx_warmup	number of warmup iterations if using approximate initialization for the LNA

Value

list with settings for elliptical slice sampling

fintzij/stemr documentation built on March 25, 2022, 12:25 p.m.