mp_jabba: Fit JABBA model

In jabbamodel/JABBA: Just Another Bayesian Biomass Assessment

Fit JABBA model

Description

Fits JABBA model in JAGS and produce output object as list()

Usage

mp_jabba(
  jbinput,
  ni = 30000,
  nt = 5,
  nb = 5000,
  nc = 2,
  init.values = FALSE,
  init.K = NULL,
  init.r = NULL,
  init.q = NULL,
  par.quantile = 0.5,
  b.quantile = 0.5,
  quickmcmc = TRUE,
  verbose = FALSE
)

Arguments

jbinput	List of input variables as output by build_jabba() MCMC settings
ni	number of iterations
nt	thinning interval of saved iterations
nb	burn-in
nc	number of mcmc chains Initial values
init.values	= FALSE,
init.K	= NULL,
init.r	= NULL,
init.q	= NULL,# vector
par.quantile	quantile(s) of parameter posterior, default median 0.5
b.quantile	quantile(s) of biomass posterior, default median 0.5
quickmcmc	option to run short mcmc
verbose	option show cat comments and progress
peels	= NULL, # retro peel option

Value

A result list containing estimates of model input, settings and results

Examples

data(iccat)
jbinput <- build_jabba(catch=iccat$bet$catch,cpue=iccat$bet$cpue,se=iccat$bet$se,model.type="Fox",verbose=FALSE)
system.time(fit_jabba(jbinput,quickmcmc=TRUE,verbose=FALSE))
system.time(mp_jabba(jbinput))

jabbamodel/JABBA documentation built on Nov. 2, 2024, 12:50 p.m.