Package: FLjjm 0.3.5

Iago Mosqueira

FLjjm: Running the JJM Stock Assessment Model Inside the MSE FLR System

Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.

Authors:Iago Mosqueira [aut, cre], Karolina Molla Gazi [aut]

FLjjm_0.3.5.tar.gz
FLjjm_0.3.5.zip(r-4.7)FLjjm_0.3.5.zip(r-4.6)FLjjm_0.3.5.zip(r-4.5)
FLjjm_0.3.5.tgz(r-4.6-any)FLjjm_0.3.5.tgz(r-4.5-any)
FLjjm_0.3.5.tar.gz(r-4.7-any)FLjjm_0.3.5.tar.gz(r-4.6-any)
FLjjm_0.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FLjjm/json (API)
NEWS

# Install 'FLjjm' in R:
install.packages('FLjjm', repos = c('https://jimianelli.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sprfmo/fljjm/issues

On CRAN:

Conda:

3.74 score 8 scripts 35 exports 104 dependencies

Last updated from:15abe9e47b. Checks:1 ERROR, 2 OK, 6 WARNING. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR496
source / vignettesOK454
linux-release-x86_64WARNING467
macos-release-arm64WARNING238
macos-oldrel-arm64WARNING227
windows-develWARNING228
windows-releaseWARNING237
windows-oldrelWARNING252
wasm-releaseOK300

Exports:buildFLBjjmbuildFLBsjjmbuildFLFsjjmbuildFLIsjjmbuildFLRPsjjmbuildFLSjjmbuildFLSsjjmbuildjjmctlbuildjjmdatacalljjmscjm.iemcjm.oemcjmage2lenexejjmsfwdmovfwdmov.omget_osgetjjmsjjmsjjms.sajmetsloadJJMSperfect.oemreadFLBjjmreadFLFsjjmreadFLIsjjmreadFLoemjjmreadFLomjjmreadFLRPsjjmreadFLSjjmreadFLSsjjmreadModreadReprunjjmsslick_performance

Dependencies:backportsbase64encbootbroombslibcachemclicodetoolscolorspacecowplotcpp11data.tabledeldirDerivdigestdoBydoFuturedplyrevaluatefarverfastmapFLasherFLBRPFLCoreFLFisheryfontawesomeforcatsforeachforecastfracdifffsfuturefuture.applygenericsggplot2ggplotFLggrepelggridgesglobalsgluegridExtragtablehighrhtmltoolsicesAdviceinterpisobanditeratorsjjmRjpegjquerylibjsonliteknitrlabelinglatticelatticeExtralifecyclelistenvlmtestmagrittrMASSMatrixmemoisemicrobenchmarkmimemodelrmsenlmennetparallellypatchworkPBSmodellingpillarpkgconfigpngprogressrpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownS7sassscalesstringistringrtibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunXMLyamlzoo

Description of the FLjjm package

Name SURNAME

Rendered fromFLjjm.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-05-31
Started: 2024-01-19

Readme and manuals

Help Manual

Help pageTopics
Combine Fisheries Model Results.combinejjmsout
Convert Age Composition to Length CompositionAgeToLengthComp
Build Functions for FLjjm Packagebuild
Build an FLBiol from a jjm.output objectbuildFLBjjm
Build FLFisheries from JJMS Model OutputbuildFLFsjjm
Construct FLIndices from a jjm.output objectbuildFLIsjjm
Build reference points (FLPar) from jjm.outputbuildFLRPsjjm
Build FLStock from jjm.outputbuildFLSjjm
Build FLStock with areas from jjm.outputbuildFLSojjm
Build multiple FLStock objects from jjm.outputbuildFLSsjjm
Updating dat and ctl file lists from FLstock(s) and FLIndicesbuildjjmctl
Calculate Total Catch across FLStockscatch,FLStocks-method
Observation Error Model wrapper for CJM within MSE workflowscjm.oem
Convert Age Composition to Length Composition for Landingscjmage2len
Converts FLQuants with Fleets as Areas into a fwdControl Objectcjmfwc
Execute JJMS Modelexejjms
Calculate Average Fishing Mortality across FLStocksfbar,FLStocks-method
FLjjm: An R Package for Interacting with JJMS Stock Assessment Model in FLRFLjjm
Forward Movement Simulationfwdmov
Forward Movement Operation Modelfwdmov.om
Run JJMS Model for Fisheries Stock Assessmentjjms
JJMS Stock Assessmentjjms.sa
Load FLStocks from JJMS ModelloadFLSjjms
Load JJMS Model ComponentsloadJJMS
Get Name of JJMS Modelnamejjms
Get Number of Stocks in JJMS ModelnStocksjjms
Clean Up JJMS Model Run Directorypackjjmsrun
Create an FLBiol from a JJMS model run directoryreadFLBjjm
Create FLFisheries objects from a JJMS model run directoryreadFLFsjjm
Create an FLIndices object from a JJMS model run directoryreadFLIsjjm
Read FLIndices with OEM iterations and MC outputsreadFLoemjjm
Create an FLombf object from a JJMS model run directoryreadFLomjjm
Create an FLPar contaning reference points from a JJMS model run directoryreadFLRPsjjm
Create an FLStock from a JJMS model run directoryreadFLSjjm
Create an FLStocks from a two-stock JJMS model run directoryreadFLSsjjm
Run JJMS Modelrunjjms
Compute performance metrics for MPs and OM in slick formatslick_performance
Calculate Total Spawning Stock Biomass across FLStocksssb,FLStocks-method
Construct Components of Fisheries ModelyourFunctionName