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New functions: MFCLWgtFit.
New classes: MFCLWgtFit.
New methods: wgtfits<-, wgtagefits<-.
New functions: read.MFCLALK, read.MFCLWgtFit.
New classes: MFCLALK.
New methods: ALK, ESS, waa<-, wgtfits, wgtagefits.
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New methods: age_length, weight_fish.
Improved read.MFCLLikelihood() so it reads in age_length likelihood.
Improved summary(MFCLLikelihood) so it reports neglogL instead of abs(neglogL) and includes cpue and age components.
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As at January 2023 - latest version in repository following adoption of skipjack MP (actual version used for evaluations will be an earlier version - see HTCondor backup folder).
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New functions: read.MFCLPseudoCatch, read.MFCLPseudoEffort.
New methods: mohns_rho.
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New functions: read.MFCLPseudoCatchEffort, read.MFCLPseudoSizeComp.
New methods: tag_shed_rate, tag_shed_rate<-.
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New functions: read.SBSBF0.
New methods: calc_diff_coffs_age_period.
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New functions: ats.
New methods: recYears.
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New functions: hcr_asymptotic, hcr_asymptotic_constrained, hcr_constrained.
New methods: mean_waa, mean_waa<-.
New functions: MFCLEquilibrium, read.MFCLEquilibrium.
New classes: MFCLEquilibrium.
New methods: Eq_calcs, Eq_calcs<-, fm_aggregated, fm_aggregated<-, YPR, YPR<-.
New functions: checkMissingRealisations, checkUnitDimnames, hcr_constant, hcr_hillary_step, hcr_threshold, hcr_threshold_constrained, MFCLLikelihood, read.MFCLLikelihood.
New classes: MFCLLikelihood.
New methods: bh_steep_contrib, bh_steep_contrib<-, catch_fish, catch_fish<-, effort_dev_penalty, effort_dev_penalty<-, fprojyr<-, length_fish, length_fish<-, q_dev_pen_fish, q_dev_pen_fish<-, q_dev_pen_fish_grp, q_dev_pen_fish_grp<-, summary, tag_rel_fish, tag_rel_fish<-, total_catch_fish, total_catch_fish<-, total_length_fish, total_length_fish<-, total_weight_fish, total_weight_fish<-.
New functions: MFCLFrq2, MFCLLenFreq2.
New methods: cateffpen, cateffpen<-, lnfrq, lnfrq<-, SB, SBF0recent, SBlatest, SBrecent, SBSBF0latest, SBSBF0recent, wtfrq, wtfrq<-.
New functions: read.MFCLSimulatedNatAge.
New classes: MFCLFrq2, MFCLLenFreq2.
New methods: as.MFCLFrq, as.MFCLFrq2, ini_version, ini_version<-, modifyRRini, region_flags, region_flags<-.
New functions: contributions.plot, hcr_constant, hcr_threshold, hcr_threshold_constrained, read.MFCLProjectedSpawningBiomass.
New methods: eval_hcr, hcr_params, hcr_params<-, SBF0Alt, SBSBF0Alt.
New functions: MFCLEMControl, MFCLMSEControl, MFCLPseudoControl, read.MFCLCatch, read.MFCLCatchN, read.MFCLPseudoAlt, write.simyears.
New classes: MFCLEMControl, MFCLMSEControl, MFCLPseudoControl.
New methods: as.MFCLLenFreq, catch_sd, catch_sd<-, doitall, doitall<-, effort_sd, effort_sd<-, hcr, hcr<-, iter, itn, itn<-, random_seeds, random_seeds<-, realisations, reduce, tag_controls, tag_controls<-.
New functions: availableMFCLversions, check.mfcl.cfg, contributions.plot, flagDiff, flagSummary, getMFCLversion, gradients, MFCLLenFit, MFCLPseudo, MFCLTagProj, qts, read.MFCLLenFit, read.MFCLProjectedNatAge, read.MFCLPseudo, read.temporary_tag_report, recPeriod, write.simNumAge.
New classes: MFCLCatch, MFCLLenFit, MFCLPseudo, MFCLTagProj.
New methods: aal, AggregateF, AggregateF<-, BBMSY, BBMSY<-, BMSY, BMSY<-, catch_obs, catch_obs<-, catch_pred, catch_pred<-, catcheff, catcheff<-, controls, controls<-, cpue_obs, cpue_obs<-, cpue_pred, cpue_pred<-, ess, ess<-, FFMSY, FFMSY<-, FMSY, FMSY<-, Fmult, Fmult<-, fprojyr, l_frq, l_frq<-, laa, lenagefits, lenagefits<-, lenfits, lenfits<-, MSY, MSY<-, orth_coffs, orth_coffs<-, plot, release_groups_proj, release_groups_proj<-, releases_proj, releases_proj<-, spp_params, spp_params<-, SPR0, subset, w_frq, w_frq<-, waa.
New functions: availableMFCLversions, check.mfcl.cfg, getMFCLversion, MFCLBase, MFCLBiol, MFCLCatch, MFCLFlags, MFCLFrq, MFCLFrqStats, MFCLIni, MFCLIniBits, MFCLLenFreq, MFCLPar, MFCLParBits, MFCLprojControl, MFCLRec, MFCLRegion, MFCLRep, MFCLSel, MFCLTag, MFCLTagRep, read.MFCLBiol, read.MFCLCatch, read.MFCLFlags, read.MFCLFrq, read.MFCLFrqStats, read.MFCLIni, read.MFCLLenFreq, read.MFCLPar, read.MFCLParBits, read.MFCLRec, read.MFCLRegion, read.MFCLRep, read.MFCLSel, read.MFCLTag, read.MFCLTagRep, setMFCLversion, setSimYrs, write.simNumAge.
New classes: MFCLBase, MFCLBiol, MFCLCatch, MFCLFlags, MFCLFrq, MFCLFrqStats, MFCLIni, MFCLIniBits, MFCLLenFreq, MFCLPar, MFCLParBits, MFCLprojControl, MFCLRec, MFCLRegion, MFCLRep, MFCLSel, MFCLTag, MFCLTagRep.
New methods: adultBiomass, adultBiomass<-, adultBiomass_nofish, adultBiomass_nofish<-, age_nage, age_nage<-, age_pars, age_pars<-, av_fish_mort_age, av_fish_mort_age<-, av_fish_mort_inst, av_fish_mort_inst<-, av_fish_mort_year, av_fish_mort_year<-, av_q_coffs, av_q_coffs<-, availability_coffs, availability_coffs<-, avyrs, avyrs<-, caeff, caeff<-, catch_dev_coffs, catch_dev_coffs<-, catch_dev_coffs_flag, catch_dev_coffs_flag<-, common_len_bias_coffs, common_len_bias_coffs<-, common_len_bias_pars, common_len_bias_pars<-, control_flags, control_flags<-, data_flags, data_flags<-, diff_coffs, diff_coffs<-, diff_coffs_age, diff_coffs_age<-, diff_coffs_age_period, diff_coffs_age_period<-, diff_coffs_age_priors, diff_coffs_age_priors<-, diff_coffs_age_ssn, diff_coffs_age_ssn<-, diff_coffs_mat, diff_coffs_mat<-, diff_coffs_nl, diff_coffs_nl<-, diff_coffs_nl_priors, diff_coffs_nl_priors<-, diff_coffs_priors, diff_coffs_priors<-, dimensions, dimensions<-, effort_dev_coffs, effort_dev_coffs<-, eq_biomass, eq_biomass<-, eq_yield, eq_yield<-, fish_params, fish_params<-, fishery_catch, fishery_catch<-, fishery_realizations, fishery_realizations<-, fishery_sel, fishery_sel<-, fishery_sel_age_comp, fishery_sel_age_comp<-, flags, flags<-, flagval, flagval<-, fm, fm<-, fm_level_devs, fm_level_devs<-, freq, freq<-, frq_age_len, frq_age_len<-, frq_version, frq_version<-, generate, generic_diffusion, generic_diffusion<-, growth, growth<-, growth_curve_devs, growth_curve_devs<-, growth_devs_age, growth_devs_age<-, growth_devs_cohort, growth_devs_cohort<-, growth_var_pars, growth_var_pars<-, ini_q_coffs, ini_q_coffs<-, lagrangian, lagrangian<-, len_bias_pars, len_bias_pars<-, lf_range, lf_range<-, log_m, log_m<-, logistic_normal_params, logistic_normal_params<-, lw_params, lw_params<-, m, m<-, m_at_age, m_at_age<-, m_devs_age, m_devs_age<-, mat, mat<-, max_grad, max_grad<-, mean_laa, mean_laa<-, mfcl, mn_len_pen, mn_len_pen<-, move_map, move_map<-, move_matrix, move_matrix<-, move_weeks, move_weeks<-, n_fisheries, n_fisheries<-, n_mean_constraints, n_mean_constraints<-, n_move_yr, n_move_yr<-, n_pars, n_pars<-, n_recs_yr, n_recs_yr<-, n_regions, n_regions<-, n_tag_groups, n_tag_groups<-, nsims, nsims<-, nyears, nyears<-, obj_fun, obj_fun<-, popN, popN<-, q0_miss, q0_miss<-, q_dev_coffs, q_dev_coffs<-, q_effdev, q_effdev<-, q_fishery, q_fishery<-, range, range<-, rec, rec<-, rec_dist, rec_dist<-, rec_init_pop_diff, rec_init_pop_diff<-, rec_month, rec_month<-, rec_obs, rec_obs<-, rec_region, rec_region<-, rec_times, rec_times<-, recaptures, recaptures<-, recoveries, recoveries<-, region_fish, region_fish<-, region_pars, region_pars<-, region_rec_var, region_rec_var<-, region_size, region_size<-, rel_ini_pop, rel_ini_pop<-, rel_rec, rel_rec<-, release_groups, release_groups<-, release_lengths, release_lengths<-, releases, releases<-, rep_rate_dev_coffs, rep_rate_dev_coffs<-, richards, richards<-, SBF0, SBSBF0, scaler, scaler<-, sd_laa, sd_laa<-, sd_length_at_age, sd_length_at_age<-, sd_length_dep, sd_length_dep<-, season_flags, season_flags<-, season_growth_pars, season_growth_pars<-, season_q_pars, season_q_pars<-, sel, sel<-, sel_dev_coffs, sel_dev_coffs2, sel_dev_coffs2<-, sel_dev_coffs<-, sel_dev_corr, sel_dev_corr<-, srr, srr<-, ssb, ssb<-, ssb_obs, ssb_obs<-, steepness, steepness<-, sv, sv<-, tag_fish_rep_flags, tag_fish_rep_flags<-, tag_fish_rep_grp, tag_fish_rep_grp<-, tag_fish_rep_pen, tag_fish_rep_pen<-, tag_fish_rep_rate, tag_fish_rep_rate<-, tag_fish_rep_target, tag_fish_rep_target<-, tag_lik, tag_lik<-, tot_pop, tot_pop<-, tot_pop_implicit, tot_pop_implicit<-, total_catch, total_catch<-, totalBiomass, totalBiomass<-, unused, unused<-, update, version, vulnBiomass, vulnBiomass<-, window, write.
General note: Unless specific news entries were written, the above entries are
based on changes in the NAMESPACE
file between versions, specifically exported
functions, classes, and methods. A simple '-' indicates that no new exports were
introduced in that version.
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