sir_control: Set parameters for SIR

View source: R/control_specification.R

sir_controlR Documentation

Set parameters for SIR

Description

Set fitting parameters for SIR with reasonable defaults.

Usage

sir_control(K_bisect_lims = c(1, 5e+05), K_bisect_tol = 1e-04,
  threshold = 1e-17, progress_bar = FALSE, verbose = 0)

Arguments

K_bisect_lims

Bounds for K when performing the bisection method of Pund and Butterworth (1995). Two-element vector denoting upper and lower bounds. Default is c(1, 5e5).

K_bisect_tol

Tolerance passed to uniroot when using the bisection method to find K.

threshold

Threshold for McCallister et al. (1994) SIR. Data specific. Defaults to 1e-17.

progress_bar

Logical; display progress bar?

verbose

Integer, defaults to 0; See Details for specifics. Note that more intermediate output will slow down sampling.

Use of progress_bar and verbose together is not allowed. If both are set, only progress_bar will be shown. The verbose argument takes an integer, controlling how much is output. All output uses message, so works with functions like supressMessages. These levels are

  • 0 no output;

  • 1 sample count and MVP violations;

  • 2 above plus likelihood totals;

  • 3 above plus likelihood components;

  • 4 above plus sampled parameter values. intermediate

Value

A list to be passed to the control argument of HUMPBACK.SIR.


antarctic-humpback-2019-assessment/HumpbackSIR documentation built on Nov. 6, 2023, 6:07 p.m.