ABItgt                  ABItgt() Computes ABI for target F, e.g. ABImsy
                        (Griffith et al. 2023)
ALK                     Convert an inverse age-length key to an
                        age-length key
ALKs                    Construct annual age-length keys
Fbrp                    Fbrp() Extract Fbrp based reference points from
                        output of computeFbrp
Fe40                    Fe40() Patterson estimator for Fmsy
Fmmy                    Fmmy() Uses opt.bisect to derive the F at
                        Maximum Median Yield from stochastic
                        simulations
Fp05                    Calculates the Fbar value giving a maximum
                        probability of ssb being below Blim of 5
                        percent
Fsim                    Fsim() Simulates stochastic stock dynamics
                        under under constant Fbrp
Fsim_grid               Stochastic forward projections over an F grid
Mlorenzen               Mlorenzen
alk.sample              Sample annual age-length keys by length class
applyALK                Convert length frequencies to numbers-at-age
applyAR                 applyAR() Function to apply ICES Advice rule
                        for F < MSY Btrigger
asem2spm                asem2spm()
bioidx.sim              generates FLIndexBiomass with random
                        observation error from an FLStock
bisect                  Bisection search for a forecast target matching
                        a performance statistic
blag                    blag()
build_gear              Build gear selectivity, F-partition and
                        sampling configurations
ca.sim                  Generate catch.n with lognormal annual and
                        multinomial age composition observation error
catch_by_gear           Relative catch by gear (fiticc()
                        'catch_by_gear' input)
catch_gear              Catch by gear and year
catch_n_gear            Partial (Baranov) catch-at-age by gear
combine_sel_age         Combine gear-specific selectivity-at-age using
                        relative apical F
computeFbrp             computeFbrp() Computes biological reference
                        points corresponding to the proxy Fbrp
computeFbrps            computeFbrps() Computes biological reference
                        points corresponding to the proxy Fbrp
condition_alk           Fold length selectivity into an inverse ALK
f_age_gear              Gear-specific fishing mortality-at-age from
                        gear Fbar trajectories
f_share_gear            Time-varying share of total F-at-age by gear
flr2stars               flr2stars()
fudc                    generates an up-down-constant F-pattern
fwd2ices                Function to summarise forecast results
fwd2stars               Function to summarise forecast results
fwd2type1               Function to summarise Type 1 GFCM fishing
                        opportunities
fwdF4B                  fwdF4B () Bisection Function to search F for a
                        given biomass
gear_ialk               Biological inverse ALK on a gear's own length
                        grid
gear_par                Extract a scalar gear entry across all gears
getF                    getF()
huecol                  huecol
iALK                    Construct an inverse age-length key
idx.sim                 generates FLIndex with lognormal annual and
                        multinomial age composition observation error
jabba2FLStockR          jabba2FLStockR()
jabba2stars             jabba2stars()
joint_sel               Joint (fleet-aggregated) selectivity-at-age
len.sim                 Simulate length-frequency samples from
                        numbers-at-age
len_grid                Length grid shared by iALK(), build_gear() and
                        all downstream helpers
lfd.sim                 Simulate a two-stage gear-specific
                        length-frequency sample
lfd.sim.season          Simulate seasonal length-frequency samples
lfd_obs_init            Initialise the LFD observations of a
                        sampling.lfd.oem() FLoem
lfd_sop                 Raise a length-frequency sample to catch weight
                        (sum of products)
lfd_template            Empty length-sample template for a gear
merge_catch             Merge catch into landings and remove discards
newselex                generates flexible 5-paramater selex curves
opt.bisect              Bisection approach to optimise x for maximising
                        y
pe_sampler              Summarise biomass process error over an F grid
pgquant                 sets plus group on FLQuant
plotAR                  plotAR Plots the new proposed ICES advice rule
plotAdvice              plotAdvice Plots stochastic stock dynamics
                        against refpts for constant Fsim()
plotCECAF               plotGFCM()
plotFsim                plotFsim Plots stochastic stock dynamics
                        against refpts for constant Fsim()
plotGFCM                plotGFCM()
plotMajuro              Plots the new proposed ICES advice rule
plotWKREF               plotWKREF Plots the newploiomass target
                        corresponding to Fbrp
plot_condALK            Heatmap of a gear's conditional inverse ALK
plot_condALK_bias       Raw vs. gear-conditioned mean length-at-age
plot_lfd_designs        Compare length-sampling designs for one year
plot_lfd_ridgeline      Plot length-frequency distributions as temporal
                        ridgelines
plot_lfd_season         Plot seasonal length-frequency distributions
plot_pe                 Plot biomass process error against B/Bmsy
plot_pf                 plot_pf()
plot_sel_a_seasonal     Compare single-timing and seasonal
                        selectivity-at-age
plot_sel_age            Plot selectivity-at-age
plot_sel_la             Plot selectivity at length and age
plotbioage              plotbioage() Plots stock N_a, W_a, M_a and
                        Mat_a by year
plotbioyr               plotbioyr() Plots stock N_a, W_a, M_a and Mat_a
                        across years
plotdyn                 plotdyn() Plots stock trajectories at age
ploteq                  ploteq() Modification of method plot('FLBRP')
                        to plot equilibrium output of computeFbrp()
plotspr                 plotspr() Plots current vs unfished spawning
                        biomass per recruit at age
pop_n_season            Calculate population numbers-at-age by season
rGclass                 Function to characterize Productivity and
                        refpts based on r and Generation
rUnif_len               Generate common random numbers for length
                        sampling
rUnif_lfd               Generate common random numbers for two-stage
                        length sampling
rc4                     r4sscol
ref.bisect              Bisection approach to find target F for B
                        (sex-structured)
rffwd                   rffwd() Project forward an FLStock with
                        evolutionary Fbar
rmultinom_crn           Draw a multinomial sample using pre-generated
                        uniform deviates (CRN-safe)
sam2FLQuant             sam2FLQuant()
sam2FLStockR            sam2FLStockR()
sam2stars               sam2stars()
sample_lfd_gears        Simulate length samples for a set of gears (one
                        area or sex)
sample_proc_dev         Sample SPM-equivalent biomass process
                        deviations from one projection
sampling.lfd.oem        Length-frequency sampling observation error
                        model
schaefer.sim            schaefer.sim()
season_fraction         Within-year distribution of the annual catch
                        over equal seasons
seasonalize_catch_n_gear
                        Disaggregate gear catch-at-age by season
sel_a_seasonal_avg      Calculate seasonally averaged
                        selectivity-at-age
sel_dnormal_len         Double-normal selectivity at length
sel_la                  Construct selectivity-at-length and
                        selectivity-at-age
sel_logistic_len        Logistic selectivity at length
sel_normal_len          Normal dome-shaped selectivity at length
sops                    scales catch-at-age to total catch with error
                        (optional)
spict2FLQuant           spict2FLQuant()
spict2FLStockR          spict2FLStockR()
spict2stars             spict2stars()
split_ess               Split a sample size exactly among seasons
spr2depletion           Equilibrium depletion implied by SPR under
                        Beverton-Holt steepness
ss2FLStockR             ss2FLStockR()
ss2ices                 ss2ices()
ss2stars                ss2stars()
ss3col                  ss3col
ss3devs                 ss3devs
ss3vcv                  ss3vcv
ssmvln                  ssmvln()
stock2ratios            stock2ratios()
stock2spm               stock2spm()
stockMedians            stockMedians() Converts FLStock into simplified
                        FLStock with Median FLQuants
survey_n_gear           Survey numbers-at-age at the time of a pulse
                        survey
updCatch.n              computes catch.n for a given harvest
updsr                   updsr()
updstars                updstars()
vbbrp                   Calculate vulnerable biomass from an FLBRP or
                        FLStock object
wt_a_seasonal           Calculate seasonally weighted weight-at-age
