Package: FLRef 1.10.9

Henning Winker

FLRef: Reference point computation for advice rules

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Authors:Henning Winker [aut, cre]

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FLRef.pdf |FLRef.html✨
FLRef/json (API)

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

Peer review:

Bug tracker:https://github.com/henning-winker/flref/issues

Datasets:

    On CRAN:

    3.36 score 3 stars 11 scripts 55 exports 54 dependencies

    Last updated 1 months agofrom:397eeee57f. Checks:OK: 1 ERROR: 6. Indexed: no.

    TargetResultDate
    Doc / VignettesOKNov 07 2024
    R-4.5-winERRORNov 07 2024
    R-4.5-linuxERRORNov 07 2024
    R-4.4-winERRORNov 07 2024
    R-4.4-macERRORNov 07 2024
    R-4.3-winERRORNov 07 2024
    R-4.3-macERRORNov 07 2024

    Exports:ABItgtalk.sampleALKsapplyALKasem2spmbioidx.simblagca.simcomputeFbrpcomputeFbrpsFbrpFe40flr2starsFmmyFp05Fsimfudcfwd2starsgetFiALKidx.simjabba2FLStockRjabba2starslen.simMlorenzennewselexopt.bisectpgquantplotAdviceplotARplotbioageplotbioyrplotdynploteqplotFsimplotMajuroplotpfplotsprplotWKREFrc4rffwdrGclassschaefer.simsopsspict2FLQuantspict2FLStockRspict2starsss2FLStockRss2starsss3colssmvlnstock2ratiosstockMediansupdsrupdstars

    Dependencies:clicodetoolscolorspacecowplotdata.tabledigestdoFuturefansifarverFLasherFLBRPFLCoreFLFisheryFLSRTMBforeachfuturefuture.applyggplot2ggplotFLggrepelglobalsgluegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmsemunsellnlmeparallellypatchworkpillarpkgconfigprogressrR6RColorBrewerRcppRcppEigenrlangscalestibbleTMButf8vctrsviridisLitewithr

    Readme and manuals

    Help Manual

    Help pageTopics
    ABItgt() Computes ABI for target F, e.g. ABImsy (Griffith et al. 2023)ABItgt
    ALK functionALK
    generates annual ALK sample with length stratified samplingalk.sample
    annual ALK functionALKs
    applyALK function to length to ageapplyALK
    asem2spm()asem2spm
    generates FLIndexBiomass with random observation error from an FLStockbioidx.sim
    blag()blag
    generates catch.n with lognormal annual and multinomial age composition observation errorca.sim
    computeFbrp() Computes biological reference points corresponding to the proxy FbrpcomputeFbrp
    computeFbrps() Computes biological reference points corresponding to the proxy FbrpcomputeFbrps
    Fbrp() Extract Fbrp based reference points from output of computeFbrpFbrp
    Fe40() Patterson estimator for FmsyFe40
    flr2stars()flr2stars
    Fmmy() Uses opt.bisect to derive the F at Maximum Median Yield from stochastic simulationsFmmy
    Calculates the Fbar value giving a maximum probability of ssb being below Blim of 5 percentFp05
    Fsim() Simulates stochastic stock dynamics under under constant FbrpFsim
    fudc()fudc
    Function to summarise forecast resultsfwd2stars
    getF()getF
    huecolhuecol
    inverse ALK function with lmin added to FLCore::invALKiALK
    generates FLIndex with lognormal annual and multinomial age composition observation erroridx.sim
    jabba2FLStockR()jabba2FLStockR
    jabba2stars()jabba2stars
    function to generate survey (pulse) and continuous LFDslen.sim
    function to generate survey (pulse) and continuous LFDslfd.sim
    MlorenzenMlorenzen
    generates flexible 5-paramater selex curvesnewselex
    Bisection approach to optimise x for maximising yopt.bisect
    sets plus group on FLQuantpgquant
    plotAdvice Plots stochastic stock dynamics against refpts for constant Fsim()plotAdvice
    plotAR Plots the new proposed ICES advice ruleplotAR
    plotbioage() Plots stock N_a, W_a, M_a and Mat_a by yearplotbioage
    plotbioyr() Plots stock N_a, W_a, M_a and Mat_a across yearsplotbioyr
    plotdyn() Plots stock trajectories at ageplotdyn
    ploteq() Modification of method plot(`FLBRP`) to plot equilibrium output of computeFbrp()ploteq
    plotFsim Plots stochastic stock dynamics against refpts for constant Fsim()plotFsim
    Plots the new proposed ICES advice ruleplotMajuro
    plotpf()plotpf
    plotspr() Plots current vs unfished spawning biomass per recruit at ageplotspr
    plotWKREF Plots the new proposed ICES advice ruleplotWKREF
    r4sscolrc4
    rffwd() Project forward an FLStock with evolutionary Fbarrffwd
    Function to characterize Productivity and refpts based on r and GenerationrGclass
    schaefer.sim()schaefer.sim
    scales catch-at-age to total catch with error (optional)sops
    spict2FLQuant()spict2FLQuant
    spict2FLStockR()spict2FLStockR
    spict2stars()spict2stars
    ss2FLStockR()ss2FLStockR
    ss2stars()ss2stars
    ss3colss3col
    ssmvln()ssmvln
    stock2ratios()stock2ratios
    stockMediansstockMedians
    updsr()updsr
    updstars()updstars