Package: FLjjm 0.2.0.9014

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_0.2.0.9014.tar.gz
FLjjm_0.2.0.9013.zip(r-4.5)FLjjm_0.2.0.9013.zip(r-4.4)FLjjm_0.2.0.9013.zip(r-4.3)
FLjjm_0.2.0.9013.tgz(r-4.5-any)FLjjm_0.2.0.9013.tgz(r-4.4-any)FLjjm_0.2.0.9013.tgz(r-4.3-any)
FLjjm_0.2.0.9013.tar.gz(r-4.5-noble)FLjjm_0.2.0.9014.tar.gz(r-4.4-noble)
FLjjm_0.2.0.9014.tgz(r-4.4-emscripten)FLjjm_0.2.0.9014.tgz(r-4.3-emscripten)
FLjjm.pdf |FLjjm.html✨
FLjjm/json (API)
NEWS

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

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

On CRAN:

Conda:

3.74 score 3 scripts 34 exports 101 dependencies

Last updated 12 days agofrom:fad0bf5e42. Checks:1 OK, 7 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 07 2025
R-4.5-winOUTDATEDMar 05 2025
R-4.5-macOUTDATEDMar 05 2025
R-4.5-linuxOUTDATEDMar 05 2025
R-4.4-winOUTDATEDMar 05 2025
R-4.4-macOUTDATEDMar 05 2025
R-4.3-winOUTDATEDMar 05 2025
R-4.3-macOUTDATEDMar 05 2025

Exports:buildFLBjjmbuildFLBsjjmbuildFLFsjjmbuildFLIsjjmbuildFLRPsjjmbuildFLSjjmbuildFLSsjjmbuildjjmctlbuildjjmdatacalljjmscjm.oemcjmage2lenexejjmsfwdmovfwdmov.omget_osgetjjmsjjmsjjms.sajmetsloadJJMSperfect.oemreadFLBjjmreadFLFsjjmreadFLIsjjmreadFLoemjjmreadFLomjjmreadFLRPsjjmreadFLSjjmreadFLSsjjmreadModreadReprunjjmsslick_performance

Dependencies:backportsbase64encbootbroombslibcachemclicodetoolscolorspacecowplotcpp11data.tabledeldirDerivdigestdoBydoFuturedoSNOWdplyrevaluatefansifarverfastmapFLasherFLBRPFLCoreFLFisheryfontawesomeforcatsforeachfsfuturefuture.applygenericsggplot2ggplotFLggrepelggridgesglobalsgluegridExtragtablehighrhtmltoolsicesAdviceinterpisobanditeratorsjjmRjpegjquerylibjsonliteknitrlabelinglatticelatticeExtralifecyclelistenvmagrittrMASSMatrixmemoisemgcvmicrobenchmarkmimemodelrmsemunsellnlmepanderparallellypatchworkPBSmodellingpillarpkgconfigpngprogressrpurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalessnowstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLyaml

Description of the FLjjm package

Name SURNAME

Rendered fromFLjjm.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2024-12-08
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
Build an FLIndices object from a jjm.output listbuildFLIsjjm
Construct an FLPar contaning reference points from a jjm.output objectbuildFLRPsjjm
Build Multiple FLStock Objects from a jjm.output ObjectbuildFLSsjjm
Updating dat and ctl file lists from FLstock(s) and FLIndicesbuildjjmctl
Calculate Total Catch across FLStockscatch,FLStocks-method
Update Observations in CJM Fishery Operation Modelcjm.oem
Update Observations in Fishery Operation Modelcjm2.oem
Convert Age Composition to Length Composition for Landingscjmage2len
Converts FLQuants with Fleets as Areas into a fwdControl Objectcjmfwc
Create a Perfect Observation Error Modelcperfect.oem
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
Perfect CJM Stock Assessmentperfcjm.sa
Create an FLBiol from a JJMS model run directoryreadFLBjjm
Create an FLFisheries from a JJMS model run directoryreadFLFsjjm
Create an FLIndices from a JJMS model run directoryreadFLIsjjm
Create an FLoem from a JJMS model run directoryreadFLoemjjm
Create an FLombf 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
Calculate Total Spawning Stock Biomass across FLStocksssb,FLStocks-method
Construct Components of Fisheries ModelyourFunctionName