Files in timjmiller/wham

Woods Hole Assessment Model (WHAM)

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.github/CONTRIBUTING.html

.github/CONTRIBUTING.md

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DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/add_basic_info.r R/check_convergence.R R/compare_wham_models.R R/fit_peel.R R/fit_tmb.R R/fit_wham.R R/get_post_samp.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/retro.R R/retro_res.R R/set_F.R R/set_M.R R/set_NAA.R R/set_WAA.R R/set_age_comp.R R/set_age_sel0.R R/set_catch.R R/set_ecov.R R/set_indices.R R/set_osa_obs.R R/set_proj.R R/set_q.R R/set_random.R R/set_selectivity.R R/wham_html.R R/wham_plots_tables.R README.md

data/vign1_m1_conv.RData

data/vign1_m2_conv.RData

data/vign1_m3_conv.RData

data/vign1_m4_conv.RData

data/vign1_res.RData

data/vign2_conv.RData

data/vign2_res.RData

data/vign3_nll_orig.RData

data/vign3_nll_proj.RData

data/vign4_conv.RData

data/vign4_res.RData

data/vign4_selAA.RData

data/vign5_res.RData

data/vign6_res.RData

data/vign8_res.RData

data/vignette_10_4_stock_om.RData

data/vignette_10_4a_stock_om_input.RData

data/vignette_10_4b_stock_om_input.RData

data/vignette_10_4c_stock_om_input.RData

data/vignette_10_4d_stock_om_input.RData

data/vignette_10_4e_stock_om_input.RData

data/vignette_10_helper.R

data/vignette_10_mod_1.RData

docs/404.html

docs/CONTRIBUTING.html

docs/LICENSE-text.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/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/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/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/retro.html

docs/reference/retro_res.html

docs/reference/set_age_sel0.html

docs/reference/wham_html.html

docs/sitemap.xml

inst/CITATION

inst/contribute/copy_ex1.R inst/contribute/copy_ex2.R inst/contribute/copy_ex3.R inst/contribute/copy_ex4.R inst/contribute/copy_ex5.R inst/contribute/copy_ex6.R inst/contribute/copy_ex8.R inst/contribute/copy_ex9.R inst/contribute/ex10_om_mse.R inst/contribute/ex1_basics.R inst/contribute/ex2_CPI_recruitment.R inst/contribute/ex3_projections.R inst/contribute/ex4_selectivity.R inst/contribute/ex5_M_GSI.R inst/contribute/ex6_NAA.R inst/contribute/ex8_compare_asap.R inst/contribute/ex9_retro_pred.R inst/contribute/par_tables.Rmd inst/contribute/run_all_examples_local.R inst/contribute/run_gdb.R inst/contribute/test_wham.R inst/contribute/test_wham_gdb.R inst/example_scripts/ex10_om_mse.R inst/example_scripts/ex11_catchability.R inst/example_scripts/ex1_basics.R inst/example_scripts/ex2_CPI_recruitment.R inst/example_scripts/ex3_projections.R inst/example_scripts/ex4_selectivity.R inst/example_scripts/ex5_M_GSI.R inst/example_scripts/ex6_NAA.R inst/example_scripts/ex8_compare_asap.R inst/example_scripts/ex9_retro_pred.R inst/example_scripts/run_all_examples.R

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/ex11_tests.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/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

man/check_convergence.Rd man/check_estimability.Rd man/compare_wham_models.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/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/retro.Rd man/retro_res.Rd man/set_age_sel0.Rd man/wham_html.Rd

pkgdown/_pkgdown.yml

pkgdown/extra.css

pkgdown/index.html

pkgdown/index.md

src/age_comp_osa.hpp

src/age_comp_sim.hpp

src/helper_functions.hpp

src/wham_v0.cpp

tests/testthat.R tests/testthat/test_age_comp_likelihoods.R tests/testthat/test_ex11_catchability.R tests/testthat/test_ex1_SNEMAYT.R tests/testthat/test_ex2_CPI_SNEMAYT.R tests/testthat/test_ex3_projections.R tests/testthat/test_ex4_selectivity.R tests/testthat/test_ex5_M.R tests/testthat/test_ex6_NAA.R tests/testthat/test_ex8_compare.R tests/testthat/test_ex9_retro_pred.R tests/testthat/test_mvtweedie.R

tests/testthat/wham_output.html

vignettes/.gitignore

vignettes/ex10_plots/looped_rep_5.png

vignettes/ex10_plots/self_fit_1_ssb.png

vignettes/ex10_plots/sim_fit_1_3d.png

vignettes/ex10_plots/sim_fit_1_4f.png

vignettes/ex10_plots/sim_fit_2_3d.png

vignettes/ex10_plots/sim_fit_2_4f.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_4d.png

vignettes/ex10_plots/sim_plot_1_4e.png

vignettes/ex10_plots/sim_plot_2_4e.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/ex1_basics.Rmd

vignettes/ex1_plots/Catch_age_comp_index1.png

vignettes/ex1_plots/Catch_age_comp_resids_index1.png

vignettes/ex1_plots/FSPR_relative.png

vignettes/ex1_plots/Index_4panel_2.png

vignettes/ex1_plots/Kobe_status.png

vignettes/ex1_plots/NAA_4panel_1.png

vignettes/ex1_plots/NAA_4panel_5.png

vignettes/ex1_plots/OSAresid_catch_4panel_fleet1.png

vignettes/ex1_plots/OSAresid_catch_4panel_index1.png

vignettes/ex1_plots/OSAresid_catch_4panel_index2.png

vignettes/ex1_plots/SPR_targets_ave_plot.png

vignettes/ex1_plots/SSB_F_trend.png

vignettes/ex1_plots/SSB_Rec_loglog.png

vignettes/ex1_plots/SSB_at_age_proportion.png

vignettes/ex1_plots/SSB_retro.png

vignettes/ex1_plots/SSB_retro_relative.png

vignettes/ex1_plots/Selectivity_fleet1.png

vignettes/ex1_plots/catch_at_age_consistency_obs_fleet1.png

vignettes/ex1_plots/catch_by_fleet.png

vignettes/ex1_plots/catch_curves_fleet1_obs.png

vignettes/ex1_plots/index.png

vignettes/ex1_plots/likelihood.png

vignettes/ex1_plots/weight_at_age_fleet1.png

vignettes/ex2_CPI_recruitment.Rmd

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/NAA_age1_retro_relative_m1.png

vignettes/ex2_plots/NAA_age1_retro_relative_m5.png

vignettes/ex2_plots/OSAresid_ecov_m4.png

vignettes/ex2_plots/OSAresid_ecov_m5.png

vignettes/ex2_plots/SSB_Rec_m3.png

vignettes/ex2_plots/SSB_Rec_m4.png

vignettes/ex3_plots/Ecov_1_proj_1.png

vignettes/ex3_plots/Ecov_1_proj_2.png

vignettes/ex3_plots/Ecov_1_proj_3.png

vignettes/ex3_plots/Ecov_1_proj_4.png

vignettes/ex3_plots/Ecov_1_proj_5.png

vignettes/ex3_plots/Kobe_status_proj_1.png

vignettes/ex3_plots/Kobe_status_proj_10.png

vignettes/ex3_plots/Kobe_status_proj_2.png

vignettes/ex3_plots/Kobe_status_proj_3.png

vignettes/ex3_plots/Kobe_status_proj_4.png

vignettes/ex3_plots/Kobe_status_proj_5.png

vignettes/ex3_plots/Kobe_status_proj_6.png

vignettes/ex3_plots/Kobe_status_proj_7.png

vignettes/ex3_plots/Kobe_status_proj_8.png

vignettes/ex3_plots/Kobe_status_proj_9.png

vignettes/ex3_plots/SSB_F_trend_proj_1.png

vignettes/ex3_plots/SSB_F_trend_proj_10.png

vignettes/ex3_plots/SSB_F_trend_proj_6.png

vignettes/ex3_plots/SSB_F_trend_proj_7.png

vignettes/ex3_plots/SSB_F_trend_proj_8.png

vignettes/ex3_plots/SSB_F_trend_proj_9.png

vignettes/ex3_projections.Rmd

vignettes/ex4_plots/selAA.png

vignettes/ex4_selectivity.Rmd vignettes/ex5_GSI_M.Rmd

vignettes/ex5_plots/MAA.png

vignettes/ex5_plots/m11_FSPR_annual_time.png

vignettes/ex5_plots/m11_FSPR_relative.png

vignettes/ex5_plots/m11_Fbar_retro_relative.png

vignettes/ex5_plots/m11_Kobe_status.png

vignettes/ex5_plots/m11_NAA_age1_retro_relative.png

vignettes/ex5_plots/m11_NAA_retro_relative.png

vignettes/ex5_plots/m11_SSB_F_trend.png

vignettes/ex5_plots/m11_SSB_retro_relative.png

vignettes/ex5_plots/m1_FSPR_annual_time.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_retro_relative.png

vignettes/ex5_plots/m1_SSB_F_trend.png

vignettes/ex5_plots/m1_SSB_retro_relative.png

vignettes/ex5_plots/m8_FSPR_annual_time.png

vignettes/ex5_plots/m8_FSPR_relative.png

vignettes/ex5_plots/m8_Fbar_retro_relative.png

vignettes/ex5_plots/m8_Kobe_status.png

vignettes/ex5_plots/m8_NAA_retro_relative.png

vignettes/ex5_plots/m8_SSB_F_trend.png

vignettes/ex5_plots/m8_SSB_retro_relative.png

vignettes/ex6_NAA.Rmd

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/ex7_debug.Rmd vignettes/ex8_compare.Rmd

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/ex9_retro_pred.Rmd

vignettes/html_screenshot.png

timjmiller/wham documentation built on Nov. 23, 2023, 2:46 a.m.