fit_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

fit_jabba(
  jbinput,
  ni = 30000,
  nt = 5,
  nb = 5000,
  nc = 2,
  init.values = FALSE,
  init.K = NULL,
  init.r = NULL,
  init.q = NULL,
  peels = NULL,
  do.ppc = TRUE,
  save.trj = TRUE,
  save.all = FALSE,
  save.jabba = FALSE,
  save.csvs = FALSE,
  output.dir = getwd(),
  quickmcmc = FALSE,
  seed = 123,
  jagsdir = NULL,
  verbose = TRUE
)

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.r	= NULL,
init.q	= NULL,# vector
peels	= NULL, # retro peel option
do.ppc	conducts and saves posterior predictive checks
save.trj	adds posteriors of stock, harvest and bk trajectories
save.all	add complete posteriors to fitted object
save.jabba	saves jabba fit as rdata object
save.csvs	option to write csv outputs
output.dir	path to save plot. default is getwd()
quickmcmc	option to run short mcmc
seed	default 123, set random by e.g. sample.int(999,1)
verbose	option show cat comments and progress
initK	= NULL,

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")
bet1 = fit_jabba(jbinput,quickmcmc=TRUE,verbose=TRUE)
jbplot_summary(bet1)

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