Files in timjmiller/wham
Woods Hole Assessment Model (WHAM)

.Rbuildignore

.gitattributes

.github/CONTRIBUTING.html

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/check_convergence.R R/compare_wham_models.R R/do_reference_points.R R/do_retro_peels.R R/do_sdreport.R R/fit_peel.R R/fit_tmb.R R/fit_wham.R R/get_post_samp.R R/initial_input_no_asap_fn.r R/jitter_wham.R R/make_html_figs_tables_fn.R R/make_osa_residuals.R R/mohns_rho.R R/par_tables_fn.R R/pipe.R R/plot_wham_output.R R/prepare_projection.R R/prepare_wham_input.R R/project_wham.R R/read_asap3_dat.R R/read_asap3_fit.R R/read_wham_fit.R R/reduce_input.R R/retro.R R/self_test.R R/set_F.R R/set_L.R R/set_M.R R/set_NAA.R R/set_WAA.R R/set_age_comp.R R/set_catch.R R/set_ecov.R R/set_indices.R R/set_move.R R/set_osa_obs.R R/set_proj.R R/set_q.R R/set_random.R R/set_selectivity.R R/verify_version.R R/wham_html.R R/wham_plots_tables.R README.md

data/vign13_res.RData

data/vign1_conv.RData

data/vign1_res.RData

data/vign2_conv.RData

data/vign2_res.RData

data/vign3_nlls.RData

data/vign4_res.RData

data/vign5_res.RData

data/vign6_res.RData

data/vign8_res.RData

data/vign_10_3.RData

data/vign_10_mod_1.RData

data/vign_12_info.RData

docs/404.html

docs/CONTRIBUTING.html

docs/LICENSE-text.html

docs/articles/ex01_basics.html

docs/articles/ex02_CPI_recruitment.html

docs/articles/ex03_projections.html

docs/articles/ex04_selectivity.html

docs/articles/ex05_GSI_M.html

docs/articles/ex05_GSI_M_files/kePrint-0.0.1/kePrint.js

docs/articles/ex05_GSI_M_files/lightable-0.0.1/lightable.css

docs/articles/ex06_NAA.html

docs/articles/ex06_NAA_files/kePrint-0.0.1/kePrint.js

docs/articles/ex06_NAA_files/lightable-0.0.1/lightable.css

docs/articles/ex07_debug.html

docs/articles/ex08_compare.html

docs/articles/ex09_retro_pred.html

docs/articles/ex10_om_mse.html

docs/articles/ex10_om_mse_files/header-attrs-2.11/header-attrs.js

docs/articles/ex10_simulation.html

docs/articles/ex11_catchability.html

docs/articles/ex11_catchability_files/header-attrs-2.11/header-attrs.js

docs/articles/ex12_multistock.html

docs/articles/ex13_no_ASAP.html

docs/articles/ex1_basics.html

docs/articles/ex1_basics_files/header-attrs-2.11/header-attrs.js

docs/articles/ex2_CPI_recruitment.html

docs/articles/ex2_CPI_recruitment_files/header-attrs-2.11/header-attrs.js

docs/articles/ex3_projections.html

docs/articles/ex3_projections_files/header-attrs-2.11/header-attrs.js

docs/articles/ex4_selectivity.html

docs/articles/ex4_selectivity_files/header-attrs-2.11/header-attrs.js

docs/articles/ex5_GSI_M.html

docs/articles/ex5_GSI_M_files/header-attrs-2.11/header-attrs.js

docs/articles/ex5_GSI_M_files/kePrint-0.0.1/kePrint.js

docs/articles/ex5_GSI_M_files/lightable-0.0.1/lightable.css

docs/articles/ex6_NAA.html

docs/articles/ex6_NAA_files/header-attrs-2.11/header-attrs.js

docs/articles/ex6_NAA_files/kePrint-0.0.1/kePrint.js

docs/articles/ex6_NAA_files/lightable-0.0.1/lightable.css

docs/articles/ex7_debug.html

docs/articles/ex7_debug_files/header-attrs-2.11/header-attrs.js

docs/articles/ex8_compare.html

docs/articles/ex8_compare_files/header-attrs-2.11/header-attrs.js

docs/articles/ex9_retro_pred.html

docs/articles/ex9_retro_pred_files/header-attrs-2.11/header-attrs.js

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/extra.css

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/check_convergence.html

docs/reference/check_estimability.html

docs/reference/compare_wham_models.html

docs/reference/do_reference_points.html

docs/reference/do_retro_peels.html

docs/reference/do_sdreport.html

docs/reference/extract_fixed.html

docs/reference/figures/badge_external_active.png

docs/reference/figures/icons8-checkmark-24-external-active.png

docs/reference/figures/icons8-email-send-24.png

docs/reference/figures/noaa-fisheries-rgb-2line-horizontal-small.png

docs/reference/fit_peel.html

docs/reference/fit_tmb.html

docs/reference/fit_wham.html

docs/reference/index.html

docs/reference/jitter_wham.html

docs/reference/make_osa_residuals.html

docs/reference/mohns_rho.html

docs/reference/pipe.html

docs/reference/plot_wham_output.html

docs/reference/prepare_projection.html

docs/reference/prepare_wham_input.html

docs/reference/project_wham.html

docs/reference/read_asap3_dat.html

docs/reference/read_asap3_fit.html

docs/reference/read_wham_fit.html

docs/reference/reduce_input.html

docs/reference/retro.html

docs/reference/retro_res.html

docs/reference/self_test.html

docs/reference/set_F.html

docs/reference/set_L.html

docs/reference/set_M.html

docs/reference/set_NAA.html

docs/reference/set_age_comp.html

docs/reference/set_age_sel0.html

docs/reference/set_catch.html

docs/reference/set_ecov.html

docs/reference/set_indices.html

docs/reference/set_move.html

docs/reference/set_osa_obs.html

docs/reference/set_q.html

docs/reference/set_selectivity.html

docs/reference/wham_html.html

docs/sitemap.xml

inst/CITATION

inst/extdata/BASE_3/ASAP3.DAT

inst/extdata/BASE_3/BASE_3.BAR

inst/extdata/BASE_3/BASE_3.BSN

inst/extdata/BASE_3/BASE_3.COR

inst/extdata/BASE_3/BASE_3.DAT

inst/extdata/BASE_3/BASE_3.LOG

inst/extdata/BASE_3/BASE_3.MCM

inst/extdata/BASE_3/BASE_3.PAR

inst/extdata/BASE_3/BASE_3.RDAT

inst/extdata/BASE_3/BASE_3.REP

inst/extdata/BASE_3/BASE_3.STD

inst/extdata/BASE_3/admb2r.log

inst/extdata/BASE_3/admodel.cov

inst/extdata/BASE_3/admodel.dep

inst/extdata/BASE_3/admodel.hes

inst/extdata/BASE_3/asap3.b01

inst/extdata/BASE_3/asap3.b02

inst/extdata/BASE_3/asap3.bar

inst/extdata/BASE_3/asap3.bsn

inst/extdata/BASE_3/asap3.cor

inst/extdata/BASE_3/asap3.eva

inst/extdata/BASE_3/asap3.log

inst/extdata/BASE_3/asap3.p01

inst/extdata/BASE_3/asap3.p02

inst/extdata/BASE_3/asap3.par

inst/extdata/BASE_3/asap3.r01

inst/extdata/BASE_3/asap3.r02

inst/extdata/BASE_3/asap3.rdat

inst/extdata/BASE_3/asap3.rep

inst/extdata/BASE_3/asap3.std

inst/extdata/BASE_3/asap3MCMC.dat

inst/extdata/BASE_3/asap3input.log

inst/extdata/BASE_3/eigv.rpt

inst/extdata/BASE_3/fmin.log

inst/extdata/BASE_3/variance

inst/extdata/CPI.csv

inst/extdata/GSI.csv

inst/extdata/age_comp_likelihood_test_values.rds

inst/extdata/ex1_SNEMAYT.dat

inst/extdata/ex1_test_results.rds

inst/extdata/ex2_SNEMAYT.dat

inst/extdata/ex2_test_results.rds

inst/extdata/ex3_test_results.rds

inst/extdata/ex4_test_results.rds

inst/extdata/ex5_summerflounder.dat

inst/extdata/ex5_test_results.rds

inst/extdata/ex6_test_results.rds

inst/extdata/ex7_SNEMAYT.dat

inst/extdata/north.dat

inst/extdata/south.dat

man/check_convergence.Rd man/check_estimability.Rd man/compare_wham_models.Rd man/do_reference_points.Rd man/do_retro_peels.Rd man/do_sdreport.Rd man/extract_fixed.Rd

man/figures/badge_external_active.png

man/figures/icons8-checkmark-24-external-active.png

man/figures/icons8-email-send-24.png

man/figures/noaa-fisheries-rgb-2line-horizontal-small.png

man/fit_peel.Rd man/fit_tmb.Rd man/fit_wham.Rd man/jitter_wham.Rd man/make_osa_residuals.Rd man/mohns_rho.Rd man/pipe.Rd man/plot_wham_output.Rd man/prepare_projection.Rd man/prepare_wham_input.Rd man/project_wham.Rd man/read_asap3_dat.Rd man/read_asap3_fit.Rd man/read_wham_fit.Rd man/reduce_input.Rd man/retro.Rd man/self_test.Rd man/set_F.Rd man/set_L.Rd man/set_M.Rd man/set_NAA.Rd man/set_age_comp.Rd man/set_catch.Rd man/set_ecov.Rd man/set_indices.Rd man/set_move.Rd man/set_osa_obs.Rd man/set_q.Rd man/set_selectivity.Rd man/wham_html.Rd

pkgdown/_pkgdown.yml

pkgdown/extra.css

pkgdown/index.html

pkgdown/index.md

src/F_Catch.hpp

src/L.hpp

src/M.hpp

src/MSY.hpp

src/Makevars

src/Makevars.win

src/N.hpp

src/PTM.hpp

src/age_comp_osa.hpp

src/age_comp_sim.hpp

src/all.hpp

src/ecov.hpp

src/helper_functions.hpp

src/move.hpp

src/multi_wham.cpp

src/projections.hpp

src/q_indices.hpp

src/selectivity.hpp

src/spr.hpp

src/tagging.hpp

vignettes/.gitignore

vignettes/ex01_basics.Rmd vignettes/ex02_CPI_recruitment.Rmd vignettes/ex03_projections.Rmd vignettes/ex04_selectivity.Rmd vignettes/ex05_GSI_M.Rmd vignettes/ex06_NAA.Rmd vignettes/ex07_debug.Rmd vignettes/ex08_compare.Rmd vignettes/ex09_retro_pred.Rmd

vignettes/ex10_plots/looped_rep_5_1.png

vignettes/ex10_plots/looped_rep_5_2.png

vignettes/ex10_plots/self_fit_1_ssb.png

vignettes/ex10_plots/sim_fit_3a.png

vignettes/ex10_plots/sim_fit_3b.png

vignettes/ex10_plots/sim_fit_3c.png

vignettes/ex10_plots/sim_fit_3d_1.png

vignettes/ex10_plots/sim_fit_3d_2.png

vignettes/ex10_plots/sim_fit_4f_1.png

vignettes/ex10_plots/sim_fit_4f_2.png

vignettes/ex10_plots/sim_plot_4d.png

vignettes/ex10_plots/sim_plot_4e_1.png

vignettes/ex10_plots/sim_plot_4e_2.png

vignettes/ex10_plots/ssb_rel_bias.png

vignettes/ex10_simulation.Rmd vignettes/ex11_catchability.Rmd

vignettes/ex11_plots/prior_posterior_q.png

vignettes/ex11_plots/q_time_series_1.png

vignettes/ex11_plots/q_time_series_2.png

vignettes/ex11_plots/q_time_series_3.png

vignettes/ex11_plots/q_time_series_4.png

vignettes/ex12_multistock.Rmd vignettes/ex13_no_ASAP.Rmd

vignettes/ex1_plots/Catch_age_comp_index_1_region_1.png

vignettes/ex1_plots/Catch_age_comp_resids_index_1.png

vignettes/ex1_plots/FSPR_absolute.png

vignettes/ex1_plots/FSPR_relative.png

vignettes/ex1_plots/Index_4panel_index_2_region_1.png

vignettes/ex1_plots/Kobe_status.png

vignettes/ex1_plots/NAA_4panel_stock_1_region_1_age_1.png

vignettes/ex1_plots/NAA_4panel_stock_1_region_1_age_5.png

vignettes/ex1_plots/OSA_resid_catch_4panel_fleet_1.png

vignettes/ex1_plots/OSA_resid_catch_4panel_index_1.png

vignettes/ex1_plots/OSA_resid_catch_4panel_index_2.png

vignettes/ex1_plots/OSA_resid_paa_6panel_fleet_1.png

vignettes/ex1_plots/OSA_resid_paa_6panel_index_1.png

vignettes/ex1_plots/OSA_resid_paa_6panel_index_2.png

vignettes/ex1_plots/SSB_F_trend.png

vignettes/ex1_plots/SSB_Rec_loglog_stock_1.png

vignettes/ex1_plots/SSB_at_age_proportion_stock_1.png

vignettes/ex1_plots/Selectivity_fleet_1_region_1.png

vignettes/ex1_plots/catch_at_age_consistency_obs_fleet_1_region_1.png

vignettes/ex1_plots/catch_by_fleet.png

vignettes/ex1_plots/catch_curves_fleet_1_region_1_obs.png

vignettes/ex1_plots/index.png

vignettes/ex1_plots/likelihood.png

vignettes/ex1_plots/stock_1_SSB_retro.png

vignettes/ex1_plots/stock_1_SSB_retro_relative.png

vignettes/ex1_plots/weight_at_age_fleet_1_fleet.png

vignettes/ex2_plots/Kobe_msy_status_m3.png

vignettes/ex2_plots/Kobe_msy_status_m4.png

vignettes/ex2_plots/Kobe_msy_status_m5.png

vignettes/ex2_plots/Kobe_msy_status_m6.png

vignettes/ex2_plots/Kobe_msy_status_m7.png

vignettes/ex2_plots/Kobe_status_m1.png

vignettes/ex2_plots/Kobe_status_m2.png

vignettes/ex2_plots/Kobe_status_m3.png

vignettes/ex2_plots/Kobe_status_m4.png

vignettes/ex2_plots/Kobe_status_m5.png

vignettes/ex2_plots/Kobe_status_m6.png

vignettes/ex2_plots/Kobe_status_m7.png

vignettes/ex2_plots/NAA_age1_retro_relative_m1.png

vignettes/ex2_plots/NAA_age1_retro_relative_m6.png

vignettes/ex2_plots/OSA_resid_ecov_4panel_CPI_m4.png

vignettes/ex2_plots/OSA_resid_ecov_4panel_CPI_m5.png

vignettes/ex2_plots/SSB_Rec_fit_m4.png

vignettes/ex2_plots/SSB_Rec_fit_m5.png

vignettes/ex2_plots/SSB_Rec_fit_m6.png

vignettes/ex2_plots/SSB_Rec_fit_m7.png

vignettes/ex3_plots/proj_10_Kobe_msy_status.png

vignettes/ex3_plots/proj_10_Kobe_status.png

vignettes/ex3_plots/proj_10_SSB_F_trend.png

vignettes/ex3_plots/proj_11_Kobe_msy_status.png

vignettes/ex3_plots/proj_11_Kobe_status.png

vignettes/ex3_plots/proj_11_SSB_F_trend.png

vignettes/ex3_plots/proj_1_Ecov_1_CPI.png

vignettes/ex3_plots/proj_1_Kobe_msy_status.png

vignettes/ex3_plots/proj_1_Kobe_status.png

vignettes/ex3_plots/proj_1_SSB_F_trend.png

vignettes/ex3_plots/proj_2_Ecov_1_CPI.png

vignettes/ex3_plots/proj_2_Kobe_msy_status.png

vignettes/ex3_plots/proj_2_Kobe_status.png

vignettes/ex3_plots/proj_2_SSB_F_trend.png

vignettes/ex3_plots/proj_3_Ecov_1_CPI.png

vignettes/ex3_plots/proj_3_Kobe_msy_status.png

vignettes/ex3_plots/proj_3_Kobe_status.png

vignettes/ex3_plots/proj_3_SSB_F_trend.png

vignettes/ex3_plots/proj_4_Ecov_1_CPI.png

vignettes/ex3_plots/proj_4_Kobe_msy_status.png

vignettes/ex3_plots/proj_4_Kobe_status.png

vignettes/ex3_plots/proj_4_SSB_F_trend.png

vignettes/ex3_plots/proj_5_Ecov_1_CPI.png

vignettes/ex3_plots/proj_5_Kobe_msy_status.png

vignettes/ex3_plots/proj_5_Kobe_status.png

vignettes/ex3_plots/proj_5_SSB_F_trend.png

vignettes/ex3_plots/proj_6_Kobe_msy_status.png

vignettes/ex3_plots/proj_6_Kobe_status.png

vignettes/ex3_plots/proj_6_SSB_F_trend.png

vignettes/ex3_plots/proj_7_Kobe_msy_status.png

vignettes/ex3_plots/proj_7_Kobe_status.png

vignettes/ex3_plots/proj_7_SSB_F_trend.png

vignettes/ex3_plots/proj_8_Kobe_msy_status.png

vignettes/ex3_plots/proj_8_Kobe_status.png

vignettes/ex3_plots/proj_8_SSB_F_trend.png

vignettes/ex3_plots/proj_9_Kobe_msy_status.png

vignettes/ex3_plots/proj_9_Kobe_status.png

vignettes/ex3_plots/proj_9_SSB_F_trend.png

vignettes/ex4_plots/selAA.png

vignettes/ex5_plots/MAA.png

vignettes/ex5_plots/m12_FSPR_absolute.png

vignettes/ex5_plots/m12_FSPR_relative.png

vignettes/ex5_plots/m12_Fbar_retro_relative.png

vignettes/ex5_plots/m12_Kobe_status.png

vignettes/ex5_plots/m12_NAA_age1_retro_relative.png

vignettes/ex5_plots/m12_NAA_retro_relative.png

vignettes/ex5_plots/m12_SSB_F_trend.png

vignettes/ex5_plots/m12_SSB_retro_relative.png

vignettes/ex5_plots/m1_FSPR_absolute.png

vignettes/ex5_plots/m1_FSPR_relative.png

vignettes/ex5_plots/m1_Fbar_retro_relative.png

vignettes/ex5_plots/m1_Kobe_status.png

vignettes/ex5_plots/m1_NAA_age1_retro_relative.png

vignettes/ex5_plots/m1_NAA_retro_relative.png

vignettes/ex5_plots/m1_SSB_F_trend.png

vignettes/ex5_plots/m1_SSB_retro_relative.png

vignettes/ex5_plots/m2_FSPR_absolute.png

vignettes/ex5_plots/m2_FSPR_relative.png

vignettes/ex5_plots/m2_Fbar_retro_relative.png

vignettes/ex5_plots/m2_Kobe_status.png

vignettes/ex5_plots/m2_NAA_age1_retro_relative.png

vignettes/ex5_plots/m2_NAA_retro_relative.png

vignettes/ex5_plots/m2_SSB_F_trend.png

vignettes/ex5_plots/m2_SSB_retro_relative.png

vignettes/ex6_plots/NAA_devs.png

vignettes/ex6_plots/m13_Ecov_1.png

vignettes/ex6_plots/m13_Fbar_retro_relative.png

vignettes/ex6_plots/m13_Kobe_status.png

vignettes/ex6_plots/m13_NAA_retro_relative.png

vignettes/ex6_plots/m13_SSB_F_trend.png

vignettes/ex6_plots/m13_SSB_retro_relative.png

vignettes/ex6_plots/m1_Ecov_1.png

vignettes/ex6_plots/m1_Fbar_retro_relative.png

vignettes/ex6_plots/m1_Kobe_status.png

vignettes/ex6_plots/m1_NAA_retro_relative.png

vignettes/ex6_plots/m1_SSB_F_trend.png

vignettes/ex6_plots/m1_SSB_retro_relative.png

vignettes/ex6_plots/m7_Ecov_1.png

vignettes/ex6_plots/m7_Fbar_retro_relative.png

vignettes/ex6_plots/m7_Kobe_status.png

vignettes/ex6_plots/m7_NAA_retro_relative.png

vignettes/ex6_plots/m7_SSB_F_trend.png

vignettes/ex6_plots/m7_SSB_retro_relative.png

vignettes/ex8_plots/compare_CV.png

vignettes/ex8_plots/compare_M_age5.png

vignettes/ex8_plots/compare_M_tile.png

vignettes/ex8_plots/compare_SSB_F_R.png

vignettes/ex8_plots/compare_ref_pts.png

vignettes/ex8_plots/compare_rel_status_kobe.png

vignettes/ex8_plots/compare_rel_status_timeseries.png

vignettes/ex8_plots/compare_sel_fleets.png

vignettes/ex8_plots/compare_sel_indices.png

vignettes/ex8_plots/compare_sel_tile.png

vignettes/ex8_plots/model_comparison.csv

vignettes/ex8_plots/res.rds

vignettes/ex8_plots/which10_2010.png

vignettes/ex8_plots/which1_noCI.png

vignettes/ex8_plots/which1_relative_colorchange.png

vignettes/ex8_plots/which1_relative_colorchange_linetype.png

vignettes/ex8_plots/which2_relative.png

vignettes/ex8_plots/which4_labels.png

vignettes/ex8_plots/which9_colorchange.png

vignettes/ex8_plots/which9_zoom.png

vignettes/ex9_plots/retro_pred_R.png

vignettes/wham_html_diagnostics.png

vignettes/wham_html_tables.png

timjmiller/wham documentation built on Feb. 4, 2025, 10:31 p.m.

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Woods Hole Assessment Model (WHAM)

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