| ABItgt() Computes ABI for target F, e.g. ABImsy (Griffith et al. 2023) | ABItgt |
| Convert an inverse age-length key to an age-length key | ALK |
| Sample annual age-length keys by length class | alk.sample |
| Construct annual age-length keys | ALKs |
| Convert length frequencies to numbers-at-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 matching a performance statistic | bisect |
| blag() | blag |
| Build gear selectivity, F-partition and sampling configurations | build_gear |
| Generate catch.n with lognormal annual and multinomial age composition observation error | ca.sim |
| Relative catch by gear (fiticc() `catch_by_gear` input) | catch_by_gear |
| Catch by gear and year | catch_gear |
| Partial (Baranov) catch-at-age by gear | catch_n_gear |
| Combine gear-specific selectivity-at-age using relative apical F | combine_sel_age |
| computeFbrp() Computes biological reference points corresponding to the proxy Fbrp | computeFbrp |
| computeFbrps() Computes biological reference points corresponding to the proxy Fbrp | computeFbrps |
| Fold length selectivity into an inverse ALK | condition_alk |
| Gear-specific fishing mortality-at-age from gear Fbar trajectories | f_age_gear |
| Time-varying share of total F-at-age by gear | f_share_gear |
| 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 |
| Stochastic forward projections over an F grid | Fsim_grid |
| 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 |
| Biological inverse ALK on a gear's own length grid | gear_ialk |
| Extract a scalar gear entry across all gears | gear_par |
| getF() | getF |
| huecol | huecol |
| Construct an inverse age-length key | iALK |
| generates FLIndex with lognormal annual and multinomial age composition observation error | idx.sim |
| jabba2FLStockR() | jabba2FLStockR |
| jabba2stars() | jabba2stars |
| Joint (fleet-aggregated) selectivity-at-age | joint_sel |
| Length grid shared by iALK(), build_gear() and all downstream helpers | len_grid |
| Simulate length-frequency samples from numbers-at-age | len.sim |
| Raise a length-frequency sample to catch weight (sum of products) | lfd_sop |
| Simulate a two-stage gear-specific length-frequency sample | lfd.sim |
| Simulate seasonal length-frequency samples | lfd.sim.season |
| Merge catch into landings and remove discards | merge_catch |
| Mlorenzen | Mlorenzen |
| generates flexible 5-paramater selex curves | newselex |
| Bisection approach to optimise x for maximising y | opt.bisect |
| Summarise biomass process error over an F grid | pe_sampler |
| sets plus group on FLQuant | pgquant |
| Heatmap of a gear's conditional inverse ALK | plot_condALK |
| Raw vs. gear-conditioned mean length-at-age | plot_condALK_bias |
| Plot length-frequency distributions as temporal ridgelines | plot_lfd_ridgeline |
| Plot seasonal length-frequency distributions | plot_lfd_season |
| Plot biomass process error against B/Bmsy | plot_pe |
| plot_pf() | plot_pf |
| Compare single-timing and seasonal selectivity-at-age | plot_sel_a_seasonal |
| Plot selectivity-at-age | plot_sel_age |
| Plot selectivity at length and age | plot_sel_la |
| 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 |
| plotGFCM() | plotCECAF |
| 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 |
| plotspr() Plots current vs unfished spawning biomass per recruit at age | plotspr |
| plotWKREF Plots the newploiomass target corresponding to Fbrp | plotWKREF |
| Calculate population numbers-at-age by season | pop_n_season |
| 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 |
| Draw a multinomial sample using pre-generated uniform deviates (CRN-safe) | rmultinom_crn |
| Generate common random numbers for length sampling | rUnif_len |
| Generate common random numbers for two-stage length sampling | rUnif_lfd |
| sam2FLQuant() | sam2FLQuant |
| sam2FLStockR() | sam2FLStockR |
| sam2stars() | sam2stars |
| Sample SPM-equivalent biomass process deviations from one projection | sample_proc_dev |
| Length-frequency sampling observation error model | sampling.lfd.oem |
| schaefer.sim() | schaefer.sim |
| Disaggregate gear catch-at-age by season | seasonalize_catch_n_gear |
| Calculate seasonally averaged selectivity-at-age | sel_a_seasonal_avg |
| Double-normal selectivity at length | sel_dnormal_len |
| Construct selectivity-at-length and selectivity-at-age | sel_la |
| Logistic selectivity at length | sel_logistic_len |
| Normal dome-shaped selectivity at length | sel_normal_len |
| scales catch-at-age to total catch with error (optional) | sops |
| spict2FLQuant() | spict2FLQuant |
| spict2FLStockR() | spict2FLStockR |
| spict2stars() | spict2stars |
| Equilibrium depletion implied by SPR under Beverton-Holt steepness | spr2depletion |
| ss2FLStockR() | ss2FLStockR |
| ss2ices() | ss2ices |
| ss2stars() | ss2stars |
| ss3col | ss3col |
| ss3devs | ss3devs |
| ss3vcv | ss3vcv |
| ssmvln() | ssmvln |
| stock2ratios() | stock2ratios |
| stock2spm() | stock2spm |
| stockMedians() Converts FLStock into simplified FLStock with Median FLQuants | stockMedians |
| computes catch.n for a given harvest | updCatch.n |
| updsr() | updsr |
| updstars() | updstars |
| Calculate vulnerable biomass from an FLBRP or FLStock object | vbbrp |
| Calculate seasonally weighted weight-at-age | wt_a_seasonal |
