Package: FLjjm 0.1.9.9011

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_0.1.9.9011.tar.gz
FLjjm_0.1.9.9011.zip(r-4.5)FLjjm_0.1.9.9011.zip(r-4.4)FLjjm_0.1.9.9011.zip(r-4.3)
FLjjm_0.1.9.9011.tgz(r-4.4-any)FLjjm_0.1.9.9011.tgz(r-4.3-any)
FLjjm_0.1.9.9011.tar.gz(r-4.5-noble)FLjjm_0.1.9.9011.tar.gz(r-4.4-noble)
FLjjm_0.1.9.9011.tgz(r-4.4-emscripten)FLjjm_0.1.9.9011.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'))

Peer review:

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

Datasets:

    On CRAN:

    32 exports 0.71 score 101 dependencies 3 scripts

    Last updated 6 months agofrom:da26edc7dd. Checks:OK: 1 WARNING: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKAug 30 2024
    R-4.5-winWARNINGAug 30 2024
    R-4.5-linuxWARNINGAug 30 2024
    R-4.4-winWARNINGAug 30 2024
    R-4.4-macWARNINGAug 30 2024
    R-4.3-winWARNINGAug 30 2024
    R-4.3-macWARNINGAug 30 2024

    Exports:buildFLBjjmbuildFLBsjjmbuildFLFsjjmbuildFLIsjjmbuildFLRPsjjmbuildFLSjjmbuildFLSsjjmbuildjjmctlbuildjjmdatacjm.oemcjm2.oemcperfect.oemexejjmsfwdmovfwdmov.omjjmsjjms.sajmetsloadJJMSperfcjm.saperfect.oemreadFLBjjmreadFLFsjjmreadFLIsjjmreadFLoemjjmreadFLomjjmreadFLRPsjjmreadFLSjjmreadFLSsjjmreadModreadReprunjjms

    Dependencies:backportsbase64encbootbroombslibcachemclicodetoolscolorspacecowplotcpp11data.tabledeldirDerivdigestdoBydoFuturedoSNOWdplyrevaluatefansifarverfastmapFLasherFLBRPFLCoreFLFisheryfontawesomeforcatsforeachfsfuturefuture.applygenericsggplot2ggplotFLggrepelggridgesglobalsgluegridExtragtablehighrhtmltoolsicesAdviceinterpisobanditeratorsjjmRjpegjquerylibjsonliteknitrlabelinglatticelatticeExtralifecyclelistenvmagrittrMASSMatrixmemoisemgcvmicrobenchmarkmimemodelrmsemunsellnlmepanderparallellypatchworkPBSmodellingpillarpkgconfigpngprogressrpurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalessnowstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLyaml

    Description of the FLjjm package

    Name SURNAME

    Rendered fromFLjjm.Rmdusingknitr::rmarkdownon Aug 30 2024.

    Last update: 2024-01-19
    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