generatePriors: generatePriors

In SOLV-Code/RapidRicker: Rapid spawner-recruit data quality checks and sensitivity tests of standard biological benchmarks.

generatePriors

Description

This function generates priors for the alternative Ricker model forms. User-specified values can be fed in for one or more variable to replace the defaults. Defaults are under development. Follow the discussion at this thread.

Usage

generatePriors(
  sr_obj,
  sr.scale = 10^6,
  model_type = "Basic",
  custom.list = NULL,
  filename = NULL,
  capacity.prior.type = "uniform"
)

Arguments

sr_obj	a data frame with Spn,Rec (actual numbers, not thousands or millions) for the MCMC and logRpS for the deterministic fit (Data for 1 Stock!). Other variables can be there but are not used (RpS, Qual, ExpF etc)
sr.scale	an integer value used to rescale the Spn and Rec variables in sr_obj, prior to the MCMC fit, default = 10^6 (i.e. convert to millions). NOTE: If sr.scale is different from 1, then the benchmark estimates are scaled back, but the MCMC estimates of alpha and beta will be in different units then the alpha and beta estimates from the deterministic fit.
model_type	one of "Basic", "Kalman", or "AR1". For details, see this wiki.
custom.list	a list with elements to replace the default values (e.g. "list(smax.in = 0.1)")
filename	either NULL, or a file/path for an output file to save the generated priors (e.g. "OUTPUT/Priors.txt")
capacity.prior.type	either "uniform" or "lognormal"

SOLV-Code/RapidRicker documentation built on Jan. 14, 2025, 9:36 a.m.