This package is considered a duplicate. The official version of this package is found at:https://flr.r-universe.dev/FLRef

Package: FLRef 1.11.12

Henning Winker

FLRef: Reference point computation for advice rules

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Authors:Henning Winker [aut, cre]

FLRef_1.11.12.tar.gz
FLRef_1.11.12.zip(r-4.7)FLRef_1.11.12.zip(r-4.6)FLRef_1.11.12.zip(r-4.5)
FLRef_1.11.12.tgz(r-4.6-any)FLRef_1.11.12.tgz(r-4.5-any)
FLRef_1.11.12.tar.gz(r-4.7-any)FLRef_1.11.12.tar.gz(r-4.6-any)
FLRef_1.11.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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:

3.55 score 3 stars 39 scripts 68 exports 47 dependencies

Last updated from:622c879fa0. Checks:7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	390
source / vignettes	OK	191
linux-release-x86_64	WARNING	395
macos-release-arm64	WARNING	220
macos-oldrel-arm64	WARNING	236
windows-devel	WARNING	360
windows-release	WARNING	335
windows-oldrel	WARNING	374
wasm-release	OK	121

Exports:ABItgt alk.sample ALKs applyALK applyAR asem2spm bioidx.sim bisect blag ca.sim computeFbrp computeFbrps Fbrp Fe40 flr2stars Fmmy Fp05 Fsim fudc fwd2ices fwd2stars fwd2type1 fwdF4B getF iALK idx.sim jabba2FLStockR jabba2stars len.sim Mlorenzen newselex opt.bisect pgquant plotAdvice plotAR plotbioage plotbioyr plotdyn ploteq plotFsim plotGFCM plotMajuro plotpf plotspr plotWKREF rc4 ref.bisect rffwd rGclass sam2FLQuant sam2FLStockR sam2stars schaefer.sim sops spict2FLQuant spict2FLStockR spict2stars ss2FLStockR ss2ices ss2stars ss3col ss3devs ss3vcv ssmvln stock2ratios stockMedians updsr updstars

Dependencies:cli codetools cowplot cpp11 data.table digest doFuture farver FLasher FLBRP FLCore FLFishery FLSRTMB foreach future future.apply ggplot2 ggplotFL ggrepel globals glue gridExtra gtable isoband iterators labeling lattice lifecycle listenv MASS Matrix mse mvtnorm parallelly patchwork progressr R6 RColorBrewer Rcpp RcppEigen rlang S7 scales TMB vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ABItgt() Computes ABI for target F, e.g. ABImsy (Griffith et al. 2023)	ABItgt
ALK function	ALK
generates annual ALK sample with length stratified sampling	alk.sample
annual ALK function	ALKs
applyALK function to length to age	applyALK
applyAR() Function to apply ICES Advice rule for F < MSY Btrigger	applyAR
asem2spm()	asem2spm
generates FLIndexBiomass with random observation error from an FLStock	bioidx.sim
Bisection search for a forecast target providing a given performance statistic value.	bisect
blag()	blag
generates catch.n with lognormal annual and multinomial age composition observation error	ca.sim
computeFbrp() Computes biological reference points corresponding to the proxy Fbrp	computeFbrp
computeFbrps() Computes biological reference points corresponding to the proxy Fbrp	computeFbrps
Fbrp() Extract Fbrp based reference points from output of computeFbrp	Fbrp
Fe40() Patterson estimator for Fmsy	Fe40
flr2stars()	flr2stars
Fmmy() Uses opt.bisect to derive the F at Maximum Median Yield from stochastic simulations	Fmmy
Calculates the Fbar value giving a maximum probability of ssb being below Blim of 5 percent	Fp05
Fsim() Simulates stochastic stock dynamics under under constant Fbrp	Fsim
generates an up-down-constant F-pattern	fudc
Function to summarise forecast results	fwd2ices
Function to summarise forecast results	fwd2stars
Function to summarise Type 1 GFCM fishing opportunities	fwd2type1
fwdF4B () Bisection Function to search F for a given biomass	fwdF4B
getF()	getF
huecol	huecol
inverse ALK function with lmin added to FLCore::invALK	iALK
generates FLIndex with lognormal annual and multinomial age composition observation error	idx.sim
jabba2FLStockR()	jabba2FLStockR
jabba2stars()	jabba2stars
function to generate survey (pulse) and continuous LFDs	len.sim
function to generate survey (pulse) and continuous LFDs	lfd.sim
Mlorenzen	Mlorenzen
generates flexible 5-paramater selex curves	newselex
Bisection approach to optimise x for maximising y	opt.bisect
sets plus group on FLQuant	pgquant
plotAdvice Plots stochastic stock dynamics against refpts for constant Fsim()	plotAdvice
plotAR Plots the new proposed ICES advice rule	plotAR
plotbioage() Plots stock N_a, W_a, M_a and Mat_a by year	plotbioage
plotbioyr() Plots stock N_a, W_a, M_a and Mat_a across years	plotbioyr
plotdyn() Plots stock trajectories at age	plotdyn
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 rule	plotMajuro
plotpf()	plotpf
plotspr() Plots current vs unfished spawning biomass per recruit at age	plotspr
plotWKREF Plots the newploiomass target corresponding to Fbrp	plotWKREF
r4sscol	rc4
Bisection approach to find target F for B (sex-structured)	ref.bisect
rffwd() Project forward an FLStock with evolutionary Fbar	rffwd
Function to characterize Productivity and refpts based on r and Generation	rGclass
sam2FLQuant()	sam2FLQuant
sam2FLStockR()	sam2FLStockR
sam2stars()	sam2stars
schaefer.sim()	schaefer.sim
scales catch-at-age to total catch with error (optional)	sops
spict2FLQuant()	spict2FLQuant
spict2FLStockR()	spict2FLStockR
spict2stars()	spict2stars
ss2FLStockR()	ss2FLStockR
ss2ices()	ss2ices
ss2stars()	ss2stars
ss3col	ss3col
ss3devs	ss3devs
ss3vcv	ss3vcv
ssmvln()	ssmvln
stock2ratios()	stock2ratios
stockMedians() Converts FLStock into simplified FLStock with Median FLQuants	stockMedians
computes catch.n for a given harvest	updCatch.n
updsr()	updsr
updstars()	updstars