Package: FLRef 1.11.4

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://flr.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/flr/flref/issues

On CRAN:

3.36 score 3 stars 11 scripts 59 exports 54 dependencies

Last updated 4 days agofrom:fe515a65cb. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 23 2025
R-4.5-winWARNINGJan 23 2025
R-4.5-linuxWARNINGJan 23 2025
R-4.4-winWARNINGJan 23 2025
R-4.4-macWARNINGJan 23 2025
R-4.3-winWARNINGJan 23 2025
R-4.3-macWARNINGJan 23 2025

Exports:ABItgtalk.sampleALKsapplyALKapplyARasem2spmbioidx.simblagca.simcomputeFbrpcomputeFbrpsFbrpFe40flr2starsFmmyFp05Fsimfudcfwd2icesfwd2starsfwdF4BgetFiALKidx.simjabba2FLStockRjabba2starslen.simMlorenzennewselexopt.bisectpgquantplotAdviceplotARplotbioageplotbioyrplotdynploteqplotFsimplotMajuroplotpfplotsprplotWKREFrc4rffwdrGclassschaefer.simsopsspict2FLQuantspict2FLStockRspict2starsss2FLStockRss2icesss2starsss3colssmvlnstock2ratiosstockMediansupdsrupdstars

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
Converts FLStock into simplified FLStock with Median FLQuantsstockMedians
updsr()updsr
updstars()updstars