The Respority includes:
The JABBA-Select source code beta version JABBA_SELECTv1.2beta.R, which is called from an assessment specific “Prime” file.
A basic simulation example JABBA_SELECT_prime_KOBsim.R. New data can be generated from a stochastic age-structured simulation model from asmsim2jabba_data.R, which calls the function OM_ccsra2jabba_Fn.R that has been adopted from the R package CCSRA.
A complex worked example JABBA_SELECT_prime_SWOss3.R that replicates the Stock Synthesis (ss3) base-case scenario of the 2017 ICCAT assessment of North Atlantic swordfish with JABBA-Select. The JABBA_SELECT_prime_SWOss3.R example illustrates how JABBA-Select can be set up for a sex-structured stock that is expoited by 11 fleets fishing with variations of logistic and dome-shaped selectivity pattern (n=6) and fitted to 9 CPUE time series of varying lengths with units given either in weight or numbers. Additional code ss2jabba_swnbase.R is provided to demonstrate how JABBA-Select input data (catch by fleet, abudance indices, life history, selectivity functions) can be extracted from a SS3 .rep file (here readily compiled as swnbase.rdata object using the R package r4ss).
JABBA requires the installation of R and JAGS.
Each JABBA-SELECT assessment requires an R Prime to read-in the input data from five comma-separated value files (.csv): (1) catch, (2) cpue, (3) se, (4) select and (5) selex; customize the stock-specific settings (e.g. Life History) and then execute the JABBA-Select source code. The R file JABBA_SELECTv1.2beta.R contains the source code of the most recent version, which is excuted via the source() function from a customized Prime file.
For further documentation also see: