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Advice rule for F < MSY Btrigger", "topics": [ "applyAR" ] }, { "page": "asem2spm", "title": "asem2spm()", "topics": [ "asem2spm" ] }, { "page": "bioidx.sim", "title": "generates FLIndexBiomass with random observation error from an FLStock", "topics": [ "bioidx.sim" ] }, { "page": "bisect", "title": "Bisection search for a forecast target matching a performance statistic", "topics": [ "bisect" ] }, { "page": "blag", "title": "blag()", "topics": [ "blag" ] }, { "page": "build_gear", "title": "Build gear selectivity, F-partition and sampling configurations", "topics": [ "build_gear" ] }, { "page": "ca.sim", "title": "Generate catch.n with lognormal annual and multinomial age composition observation error", "topics": [ "ca.sim" ] }, { "page": "catch_by_gear", "title": "Relative catch by gear (fiticc() `catch_by_gear` input)", "topics": [ "catch_by_gear" ] }, { "page": "catch_gear", "title": "Catch by gear and year", "topics": [ "catch_gear" ] }, { "page": "catch_n_gear", "title": "Partial (Baranov) catch-at-age by gear", "topics": [ "catch_n_gear" ] }, { "page": "combine_sel_age", "title": "Combine gear-specific selectivity-at-age using relative apical F", "topics": [ "combine_sel_age" ] }, { "page": "computeFbrp", "title": "computeFbrp() Computes biological reference points corresponding to the proxy Fbrp", "topics": [ "computeFbrp" ] }, { "page": "computeFbrps", "title": "computeFbrps() Computes biological reference points corresponding to the proxy Fbrp", "topics": [ "computeFbrps" ] }, { "page": "condition_alk", "title": "Fold length selectivity into an inverse ALK", "topics": [ "condition_alk" ] }, { "page": "f_age_gear", "title": "Gear-specific fishing mortality-at-age from gear Fbar trajectories", "topics": [ "f_age_gear" ] }, { "page": "f_share_gear", "title": "Time-varying share of total F-at-age by gear", "topics": [ "f_share_gear" ] }, { "page": "Fbrp", "title": "Fbrp() Extract Fbrp based reference points from output of computeFbrp", "topics": [ "Fbrp" ] }, { "page": "Fe40", "title": "Fe40() Patterson estimator for Fmsy", "topics": [ "Fe40" ] }, { "page": "flr2stars", "title": "flr2stars()", "topics": [ "flr2stars" ] }, { "page": "Fmmy", "title": "Fmmy() Uses opt.bisect to derive the F at Maximum Median Yield from stochastic simulations", "topics": [ "Fmmy" ] }, { "page": "Fp05", "title": "Calculates the Fbar value giving a maximum probability of ssb being below Blim of 5 percent", "topics": [ "Fp05" ] }, { "page": "Fsim", "title": "Fsim() Simulates stochastic stock dynamics under under constant Fbrp", "topics": [ "Fsim" ] }, { "page": "Fsim_grid", "title": "Stochastic forward projections over an F grid", "topics": [ "Fsim_grid" ] }, { "page": "fudc", "title": "generates an up-down-constant F-pattern", "topics": [ "fudc" ] }, { "page": "fwd2ices", "title": "Function to summarise forecast results", "topics": [ "fwd2ices" ] }, { "page": "fwd2stars", "title": "Function to summarise forecast results", "topics": [ "fwd2stars" ] }, { "page": "fwd2type1", "title": "Function to summarise Type 1 GFCM fishing opportunities", "topics": [ "fwd2type1" ] }, { "page": "fwdF4B", "title": "fwdF4B () Bisection Function to search F for a given biomass", "topics": [ "fwdF4B" ] }, { "page": "gear_ialk", "title": "Biological inverse ALK on a gear's own length grid", "topics": [ "gear_ialk" ] }, { "page": "gear_par", "title": "Extract a scalar gear entry across all gears", "topics": [ "gear_par" ] }, { "page": "getF", "title": "getF()", "topics": [ "getF" ] }, { "page": "huecol", "title": "huecol", "topics": [ "huecol" ] }, { "page": "iALK", "title": "Construct an inverse age-length key", "topics": [ "iALK" ] }, { "page": "idx.sim", "title": "generates FLIndex with lognormal annual and multinomial age composition observation error", "topics": [ "idx.sim" ] }, { "page": "jabba2FLStockR", "title": "jabba2FLStockR()", "topics": [ "jabba2FLStockR" ] }, { "page": "jabba2stars", "title": "jabba2stars()", "topics": [ "jabba2stars" ] }, { "page": "joint_sel", "title": "Joint (fleet-aggregated) selectivity-at-age", "topics": [ "joint_sel" ] }, { "page": "len_grid", "title": "Length grid shared by iALK(), build_gear() and all downstream helpers", "topics": [ "len_grid" ] }, { "page": "len.sim", "title": "Simulate length-frequency samples from numbers-at-age", "topics": [ "len.sim" ] }, { "page": "lfd_obs_init", "title": "Initialise the LFD observations of a sampling.lfd.oem() FLoem", "topics": [ "lfd_obs_init" ] }, { "page": "lfd_sop", "title": "Raise a length-frequency sample to catch weight (sum of products)", "topics": [ "lfd_sop" ] }, { "page": "lfd_template", "title": "Empty length-sample template for a gear", "topics": [ "lfd_template" ] }, { "page": "lfd.sim", "title": "Simulate a two-stage gear-specific length-frequency sample", "topics": [ "lfd.sim" ] }, { "page": "lfd.sim.season", "title": "Simulate seasonal length-frequency samples", "topics": [ "lfd.sim.season" ] }, { "page": "merge_catch", "title": "Merge catch into landings and remove discards", "topics": [ "merge_catch" ] }, { "page": "Mlorenzen", "title": "Mlorenzen", "topics": [ "Mlorenzen" ] }, { "page": "newselex", "title": "generates flexible 5-paramater selex curves", "topics": [ "newselex" ] }, { "page": "opt.bisect", "title": "Bisection approach to optimise x for maximising y", "topics": [ "opt.bisect" ] }, { "page": "pe_sampler", "title": "Summarise biomass process error over an F grid", "topics": [ "pe_sampler" ] }, { "page": "pgquant", "title": "sets plus group on FLQuant", "topics": [ "pgquant" ] }, { "page": "plot_condALK", "title": "Heatmap of a gear's conditional inverse ALK", "topics": [ "plot_condALK" ] }, { "page": "plot_condALK_bias", "title": "Raw vs. gear-conditioned mean length-at-age", "topics": [ "plot_condALK_bias" ] }, { "page": "plot_lfd_designs", "title": "Compare length-sampling designs for one year", "topics": [ "plot_lfd_designs" ] }, { "page": "plot_lfd_ridgeline", "title": "Plot length-frequency distributions as temporal ridgelines", "topics": [ "plot_lfd_ridgeline" ] }, { "page": "plot_lfd_season", "title": "Plot seasonal length-frequency distributions", "topics": [ "plot_lfd_season" ] }, { "page": "plot_pe", "title": "Plot biomass process error against B/Bmsy", "topics": [ "plot_pe" ] }, { "page": "plot_pf", "title": "plot_pf()", "topics": [ "plot_pf" ] }, { "page": "plot_sel_a_seasonal", "title": "Compare single-timing and seasonal selectivity-at-age", "topics": [ "plot_sel_a_seasonal" ] }, { "page": "plot_sel_age", "title": "Plot selectivity-at-age", "topics": [ "plot_sel_age" ] }, { "page": "plot_sel_la", "title": "Plot selectivity at length and age", "topics": [ "plot_sel_la" ] }, { "page": "plotAdvice", "title": "plotAdvice Plots stochastic stock dynamics against refpts for constant Fsim()", "topics": [ "plotAdvice" ] }, { "page": "plotAR", "title": "plotAR Plots the new proposed ICES advice rule", "topics": [ "plotAR" ] }, { "page": "plotbioage", "title": "plotbioage() Plots stock N_a, W_a, M_a and Mat_a by year", "topics": [ "plotbioage" ] }, { "page": "plotbioyr", "title": "plotbioyr() Plots stock N_a, W_a, M_a and Mat_a across years", "topics": [ "plotbioyr" ] }, { "page": "plotCECAF", "title": "plotGFCM()", "topics": [ "plotCECAF" ] }, { "page": "plotdyn", "title": "plotdyn() Plots stock trajectories at age", "topics": [ "plotdyn" ] }, { "page": "ploteq", "title": "ploteq() Modification of method plot(`FLBRP`) to plot equilibrium output of computeFbrp()", "topics": [ "ploteq" ] }, { "page": "plotFsim", "title": "plotFsim Plots stochastic stock dynamics against refpts for constant Fsim()", "topics": [ "plotFsim" ] }, { "page": "plotGFCM", "title": "plotGFCM()", "topics": [ "plotGFCM" ] }, { "page": "plotMajuro", "title": "Plots the new proposed ICES advice rule", "topics": [ "plotMajuro" ] }, { "page": "plotspr", "title": "plotspr() Plots current vs unfished spawning biomass per recruit at age", "topics": [ "plotspr" ] }, { "page": "plotWKREF", "title": "plotWKREF Plots the newploiomass target corresponding to Fbrp", "topics": [ "plotWKREF" ] }, { "page": "pop_n_season", "title": "Calculate population numbers-at-age by season", "topics": [ "pop_n_season" ] }, { "page": "rc4", "title": "r4sscol", "topics": [ "rc4" ] }, { "page": "ref.bisect", "title": "Bisection approach to find target F for B (sex-structured)", "topics": [ "ref.bisect" ] }, { "page": "rffwd", "title": "rffwd() Project forward an FLStock with evolutionary Fbar", "topics": [ "rffwd" ] }, { "page": "rGclass", "title": "Function to characterize Productivity and refpts based on r and Generation", "topics": [ "rGclass" ] }, { "page": "rmultinom_crn", "title": "Draw a multinomial sample using pre-generated uniform deviates (CRN-safe)", "topics": [ "rmultinom_crn" ] }, { "page": "rUnif_len", "title": "Generate common random numbers for length sampling", "topics": [ "rUnif_len" ] }, { "page": "rUnif_lfd", "title": "Generate common random numbers for two-stage length sampling", "topics": 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[ "seasonalize_catch_n_gear" ] }, { "page": "sel_a_seasonal_avg", "title": "Calculate seasonally averaged selectivity-at-age", "topics": [ "sel_a_seasonal_avg" ] }, { "page": "sel_dnormal_len", "title": "Double-normal selectivity at length", "topics": [ "sel_dnormal_len" ] }, { "page": "sel_la", "title": "Construct selectivity-at-length and selectivity-at-age", "topics": [ "sel_la" ] }, { "page": "sel_logistic_len", "title": "Logistic selectivity at length", "topics": [ "sel_logistic_len" ] }, { "page": "sel_normal_len", "title": "Normal dome-shaped selectivity at length", "topics": [ "sel_normal_len" ] }, { "page": "sops", "title": "scales catch-at-age to total catch with error (optional)", "topics": [ "sops" ] }, { "page": "spict2FLQuant", "title": "spict2FLQuant()", "topics": [ "spict2FLQuant" ] }, { "page": "spict2FLStockR", "title": "spict2FLStockR()", "topics": [ "spict2FLStockR" ] }, { "page": "spict2stars", "title": "spict2stars()", "topics": [ "spict2stars" ] }, { "page": 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