Description of the FLjjm package

Using the FLjjm package

Loading jjms outputs

       readFLBjjm           FLomBF
model ------------- FLBiol ---------- OM (FLomBF)
       |-- jjmR::readJJM    |-- biol
       `-- buildFLBjjm      |-- fisheries
                            `-- refpts 
       `----------- buildFLomFB ------------|

Running jjms

        cjm.oem            buildjjm              writeJJM          exejjms
FLomBF --------- FLStock  ---------- jjm.output ---------- mod.dat -------- model
       |         FLIndices                                 mod.ctl
       |-- buildjjmdat
       `-- buildjjmctl
                                      `-------------- runjjms -----------------|
                  `---------------------- jjms --------------------------------|

jjms.sa

jjms
└── runjjms
    └── exejjms
        │── calljjms
        └── packjjmsrun

Observation Error Model (oem)

Indices of abundance to generate in MP:

  • Chile_AcousN
  • Chile_CPUE
  • Peru_CPUE
  • Offshore_CPUE

Example / Workflow 1

Example / Workflow 2

Reference

buildjjmdata

buildFLIsjjm

  • Creates and object of class FLIndices containing the indices of abundance used in the jjms model runs.

FLIndex

More information

Software Versions

  • R version 4.6.0 (2026-04-24)
  • FLCore: 2.6.30
  • FLjjm: 0.3.6
  • jjmR: 1.2020.1
  • Compiled: Wed Jun 10 11:48:07 2026
  • Git Hash: f27edb9

Author information

  • Name SURNAME. Affiliation. Address, Locality (RE) Country.
  • Name SURNAME. Affiliation. Address, Locality (RE) Country.
  • Name SURNAME. Affiliation. Address, Locality (RE) Country.

References