Reference point computation for advice rules
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Documentation for package ‘FLRef’ version 1.14
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A B C F G H I J L M N O P R S U V W
-- A --
| 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 |
| alk.sample | Sample annual age-length keys by length class |
| ALKs | Construct annual age-length keys |
| applyALK | Convert length frequencies to numbers-at-age |
| applyAR | applyAR() Function to apply ICES Advice rule for F < MSY Btrigger |
| asem2spm | asem2spm() |
-- B --
| 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 |
-- C --
| 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 --
| Fbrp | Fbrp() Extract Fbrp based reference points from output of computeFbrp |
| Fe40 | Fe40() Patterson estimator for Fmsy |
| flr2stars | flr2stars() |
| 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 |
| 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 |
| 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 |
-- G --
| gear_ialk | Biological inverse ALK on a gear's own length grid |
| gear_par | Extract a scalar gear entry across all gears |
| getF | getF() |
-- H --
| huecol | huecol |
-- I --
| iALK | Construct an inverse age-length key |
| idx.sim | generates FLIndex with lognormal annual and multinomial age composition observation error |
-- J --
| jabba2FLStockR | jabba2FLStockR() |
| jabba2stars | jabba2stars() |
| joint_sel | Joint (fleet-aggregated) selectivity-at-age |
-- L --
| 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 |
-- M --
| merge_catch | Merge catch into landings and remove discards |
| Mlorenzen | Mlorenzen |
-- N --
| newselex | generates flexible 5-paramater selex curves |
-- O --
| opt.bisect | Bisection approach to optimise x for maximising y |
-- P --
| pe_sampler | Summarise biomass process error over an F grid |
| pgquant | sets plus group on FLQuant |
| plotAdvice | plotAdvice Plots stochastic stock dynamics against refpts for constant Fsim() |
| plotAR | plotAR Plots the new proposed ICES advice rule |
| 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 |
| plotCECAF | plotGFCM() |
| plotdyn | plotdyn() Plots stock trajectories at age |
| ploteq | ploteq() Modification of method plot('FLBRP') to plot equilibrium output of computeFbrp() |
| plotFsim | plotFsim Plots stochastic stock dynamics against refpts for constant Fsim() |
| plotGFCM | plotGFCM() |
| plotMajuro | Plots the new proposed ICES advice rule |
| plotspr | plotspr() Plots current vs unfished spawning biomass per recruit at age |
| 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_age | Plot selectivity-at-age |
| plot_sel_a_seasonal | Compare single-timing and seasonal selectivity-at-age |
| plot_sel_la | Plot selectivity at length and age |
| pop_n_season | Calculate population numbers-at-age by season |
-- R --
| rc4 | r4sscol |
| ref.bisect | Bisection approach to find target F for B (sex-structured) |
| rffwd | rffwd() Project forward an FLStock with evolutionary Fbar |
| rGclass | Function to characterize Productivity and refpts based on r and Generation |
| rmultinom_crn | Draw a multinomial sample using pre-generated uniform deviates (CRN-safe) |
| rUnif_len | Generate common random numbers for length sampling |
| rUnif_lfd | Generate common random numbers for two-stage length sampling |
-- S --
| 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() |
| seasonalize_catch_n_gear | Disaggregate gear catch-at-age by season |
| season_fraction | Within-year distribution of the annual catch over equal seasons |
| 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 |
-- U --
| updCatch.n | computes catch.n for a given harvest |
| updsr | updsr() |
| updstars | updstars() |
-- V --
| vbbrp | Calculate vulnerable biomass from an FLBRP or FLStock object |
-- W --
| wt_a_seasonal | Calculate seasonally weighted weight-at-age |