Package: FLRef 1.11.13

Henning Winker

FLRef: Reference point computation for advice rules

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Authors:Henning Winker [aut, cre]

FLRef_1.11.13.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
FLRef/json (API)

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

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

On CRAN:

Conda:

3.68 score 3 stars 40 scripts 82 exports 47 dependencies

Last updated from:dfdcc55715. Checks:2 ERROR, 2 OK, 5 WARNING. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR217
source / vignettesOK194
linux-release-x86_64WARNING392
macos-release-arm64WARNING329
macos-oldrel-arm64WARNING359
windows-develERROR154
windows-releaseWARNING351
windows-oldrelWARNING343
wasm-releaseOK130

Exports:ABItgtalk.sampleALKsapplyALKapplyARasem2spmbioidx.simbisectblagca.simcombine_sel_agecomputeFbrpcomputeFbrpsFbrpFe40flr2starsFmmyFp05FsimFsim_gridfudcfwd2icesfwd2starsfwd2type1fwdF4BgetFiALKidx.simjabba2FLStockRjabba2starslen.simmerge_catchMlorenzennewselexopt.bisectpe_samplerpgquantplot_peplot_pfplot_sel_ageplot_sel_laplotAdviceplotARplotbioageplotbioyrplotdynploteqplotFsimplotGFCMplotMajuroplotsprplotWKREFrc4ref.bisectrffwdrGclasssam2FLQuantsam2FLStockRsam2starssample_proc_devschaefer.simsel_dnormal_lensel_lasel_logistic_lensel_normal_lensopsspict2FLQuantspict2FLStockRspict2starsss2FLStockRss2icesss2starsss3colss3devsss3vcvssmvlnstock2ratiosstock2spmstockMediansupdsrupdstarsvbbrp

Dependencies:clicodetoolscowplotcpp11data.tabledigestdoFuturefarverFLasherFLBRPFLCoreFLFisheryFLSRTMBforeachfuturefuture.applyggplot2ggplotFLggrepelglobalsgluegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvMASSMatrixmsemvtnormparallellypatchworkprogressrR6RColorBrewerRcppRcppEigenrlangS7scalesTMBvctrsviridisLitewithr

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
applyAR() Function to apply ICES Advice rule for F < MSY BtriggerapplyAR
asem2spm()asem2spm
generates FLIndexBiomass with random observation error from an FLStockbioidx.sim
Bisection search for a forecast target matching a performance statisticbisect
blag()blag
generates catch.n with lognormal annual and multinomial age composition observation errorca.sim
Combine gear-specific selectivity-at-age using relative apical Fcombine_sel_age
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
Stochastic forward projections over an F gridFsim_grid
generates an up-down-constant F-patternfudc
Function to summarise forecast resultsfwd2ices
Function to summarise forecast resultsfwd2stars
Function to summarise Type 1 GFCM fishing opportunitiesfwd2type1
fwdF4B () Bisection Function to search F for a given biomassfwdF4B
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
Merge catch into landings and remove discardsmerge_catch
MlorenzenMlorenzen
generates flexible 5-paramater selex curvesnewselex
Bisection approach to optimise x for maximising yopt.bisect
Summarise biomass process error over an F gridpe_sampler
sets plus group on FLQuantpgquant
Plot biomass process error against B/Bmsyplot_pe
plot_pf()plot_pf
Plot selectivity-at-ageplot_sel_age
Plot selectivity at length and ageplot_sel_la
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
plotGFCM()plotCECAF
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
plotGFCM()plotGFCM
Plots the new proposed ICES advice ruleplotMajuro
plotspr() Plots current vs unfished spawning biomass per recruit at ageplotspr
plotWKREF Plots the newploiomass target corresponding to FbrpplotWKREF
r4sscolrc4
Bisection approach to find target F for B (sex-structured)ref.bisect
rffwd() Project forward an FLStock with evolutionary Fbarrffwd
Function to characterize Productivity and refpts based on r and GenerationrGclass
sam2FLQuant()sam2FLQuant
sam2FLStockR()sam2FLStockR
sam2stars()sam2stars
Sample SPM-equivalent biomass process deviations from one projectionsample_proc_dev
schaefer.sim()schaefer.sim
Double-normal selectivity at lengthsel_dnormal_len
Generate selectivity-at-length and selectivity-at-agesel_la
Logistic selectivity at lengthsel_logistic_len
Normal dome-shaped selectivity at lengthsel_normal_len
scales catch-at-age to total catch with error (optional)sops
spict2FLQuant()spict2FLQuant
spict2FLStockR()spict2FLStockR
spict2stars()spict2stars
ss2FLStockR()ss2FLStockR
ss2ices()ss2ices
ss2stars()ss2stars
ss3colss3col
ss3devsss3devs
ss3vcvss3vcv
ssmvln()ssmvln
stock2ratios()stock2ratios
stock2spm()stock2spm
stockMedians() Converts FLStock into simplified FLStock with Median FLQuantsstockMedians
computes catch.n for a given harvestupdCatch.n
updsr()updsr
updstars()updstars
Calculate vulnerable biomass from an FLBRP or FLStock objectvbbrp