Files in pbs-assess/gfiscamutils
Provide functions for iSCAM models
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/autocorr-plot.R
R/batman.R
R/calc-logs.R
R/calc-mcmc.R
R/calc-mpd-logs.R
R/calc-probs-biomass.R
R/calc-quantiles.R
R/create-rds-file.R
R/delete-files-ext.R
R/extract-age-output.R
R/extract-area-sex-matrices.R
R/extract-group-matrices.R
R/fetch-file-names.R
R/find-f-b40.R
R/fix-m.R
R/get-estimated-params.R
R/get-proj-depl.R
R/gfiscamutils.R
R/iscam-filenames.R
R/load-iscam-files.R
R/load-longer.R
R/load-selfit-file.R
R/mcmc-diagnostics.R
R/mcmc-thin.R
R/model-setup.R
R/plot-age-fits-mcmc.R
R/plot-age-fits-mpd.R
R/plot-age-resids-boxes-mcmc.R
R/plot-age-resids-mcmc.R
R/plot-age-resids-mpd.R
R/plot-autocorr-mcmc.R
R/plot-biomass-grid-mcmc.R
R/plot-biomass-mcmc.R
R/plot-biomass-mpd.R
R/plot-biomass-proj-mcmc.R
R/plot-biomass-proj-mpd.R
R/plot-catch-fit-mcmc.R
R/plot-catch-fleet.R
R/plot-distribution.R
R/plot-f-mcmc.R
R/plot-index-mcmc.R
R/plot-index-mpd.R
R/plot-pairs-mcmc.R
R/plot-param-stats-mcmc.R
R/plot-priors-posts-mcmc.R
R/plot-q-mcmc.R
R/plot-rdevs-mcmc.R
R/plot-recr-grid-mcmc.R
R/plot-recr-mcmc.R
R/plot-recr-mpd.R
R/plot-ref-points-dist-mcmc.R
R/plot-ref-points.R
R/plot-selex-gear-mcmc.R
R/plot-selex-gear-mpd.R
R/plot-selex-mcmc.R
R/plot-selex-mpd.R
R/plot-sr-mcmc.R
R/plot-traces-mcmc.R
R/plot-ts-mcmc.R
R/plot-vuln-mcmc.R
R/plot-weight-at-age.R
R/read-control-file.R
R/read-data-file.R
R/read-list.R
R/read-mcmc.R
R/read-par-file.R
R/read-projection-file.R
R/read-report-file.R
R/rename_gear_iscam.R
R/replace-gear-names.R
R/run-iscam.R
R/run-retrospectives.R
R/set-dirs.R
R/set-gear-language.R
R/standardize-props.R
R/table-bio-depl.R
R/table-catch-area.R
R/table-catch-fleets.R
R/table-catch.R
R/table-decision.R
R/table-decisions.R
R/table-growth-params.R
R/table-index-values.R
R/table-iscam-param-desc.R
R/table-likelihood.R
R/table-param-est-mcmc.R
R/table-param-est-mpd.R
R/table-param-phi-mpd.R
R/table-param-settings.R
R/table-ref-points-mcmc.R
R/table-ref-rate.R
R/table-selectivity.R
R/table-sens-params.R
R/table-sens-q.R
R/table-ts-values.R
R/themes.R
R/utilities.R
R/utils-convert-prob-cols-language.R
R/write-projection-file.R
R/zzz.R
README.md
data-raw/generate-package-data.R
data/dos.append.to.log.rda
data/dos.pipe.to.log.rda
data/iscam.exe.file.rda
data/iscam.starter.file.rda
data/iscam_palette.rda
data/linux.append.to.log.rda
data/linux.pipe.to.log.rda
data/log.file.rda
data/mcmc.age.fits.file.rda
data/mcmc.age.resids.file.rda
data/mcmc.biomass.file.rda
data/mcmc.catch.file.rda
data/mcmc.file.rda
data/mcmc.fishing.mort.file.rda
data/mcmc.fishing.mort.u.file.rda
data/mcmc.index.fits.file.rda
data/mcmc.index.resids.file.rda
data/mcmc.index.standardized.resids.file.rda
data/mcmc.natural.mort.file.rda
data/mcmc.proj.file.rda
data/mcmc.recr.devs.file.rda
data/mcmc.recr.file.rda
data/mcmc.sel.female.file.rda
data/mcmc.sel.file.rda
data/mcmc.sel.male.file.rda
data/mcmc.sr.file.rda
data/mcmc.vuln.biomass.file.rda
data/mdl_cls.rda
data/mdl_grp_cls.rda
data/mdl_lst_cls.rda
data/model.class.rda
data/model.lst.class.rda
data/mpd.proj.file.rda
data/output.files.rda
data/par.file.rda
data/rdata.file.rda
data/rep.file.rda
data/retro.dir.rda
gfiscamutils.Rproj
man/autocorr_plot.Rd
man/batman.Rd
man/c.model.list.Rd
man/calc_beta_mean_cv.Rd
man/calc_beta_params.Rd
man/calc_logs.Rd
man/calc_longer_quants.Rd
man/calc_mcmc.Rd
man/calc_mpd_logs.Rd
man/calc_probs_biomass.Rd
man/calc_quantiles.Rd
man/calc_rho_vartheta.Rd
man/calc_sig_tau.Rd
man/convert_prob_cols_language.Rd
man/create_rds_file.Rd
man/delete_files_ext.Rd
man/dos.append.to.log.Rd
man/dos.pipe.to.log.Rd
man/extract_age_output.Rd
man/extract_area_sex_matrices.Rd
man/extract_group_matrices.Rd
man/fetch_file_names.Rd
man/find_f_b40.Rd
man/fix_m.Rd
man/gear_lu_table.Rd
man/get_estimated_params.Rd
man/get_fancy_expr.Rd
man/get_fancy_names.Rd
man/get_group_parvals.Rd
man/get_num_params_est.Rd
man/get_parvals.Rd
man/get_proj_biomass_raw.Rd
man/gfiscam_theme.Rd
man/gfiscamutils.Rd
man/is_iscam_model.Rd
man/is_iscam_model_group.Rd
man/is_iscam_model_list.Rd
man/iscam.exe.file.Rd
man/iscam.starter.file.Rd
man/iscam_palette.Rd
man/likelihood_table.Rd
man/linux.append.to.log.Rd
man/linux.pipe.to.log.Rd
man/load_iscam_files.Rd
man/load_longer.Rd
man/load_rds_file.Rd
man/load_selest.Rd
man/log.file.Rd
man/make.likelihood.table.Rd
man/mcmc.age.fits.file.Rd
man/mcmc.age.resids.file.Rd
man/mcmc.biomass.file.Rd
man/mcmc.catch.file.Rd
man/mcmc.file.Rd
man/mcmc.fishing.mort.file.Rd
man/mcmc.fishing.mort.u.file.Rd
man/mcmc.index.fits.file.Rd
man/mcmc.index.resids.file.Rd
man/mcmc.index.standardized.resids.file.Rd
man/mcmc.natural.mort.file.Rd
man/mcmc.proj.file.Rd
man/mcmc.recr.devs.file.Rd
man/mcmc.recr.file.Rd
man/mcmc.sel.female.file.Rd
man/mcmc.sel.file.Rd
man/mcmc.sel.male.file.Rd
man/mcmc.sr.file.Rd
man/mcmc.vuln.biomass.file.Rd
man/mcmc_thin.Rd
man/mdl_cls.Rd
man/mdl_grp_cls.Rd
man/mdl_lst_cls.Rd
man/model.class.Rd
man/model.lst.class.Rd
man/model_setup.Rd
man/modify_model_path.Rd
man/move_legend_to_empty_facet.Rd
man/mpd.proj.file.Rd
man/output.files.Rd
man/par.file.Rd
man/plot_age_fits_mcmc.Rd
man/plot_age_fits_mpd.Rd
man/plot_age_resids_boxes_mcmc.Rd
man/plot_age_resids_mcmc.Rd
man/plot_age_resids_mpd.Rd
man/plot_autocorr_mcmc.Rd
man/plot_biomass_grid_mcmc.Rd
man/plot_biomass_mcmc.Rd
man/plot_biomass_mpd.Rd
man/plot_biomass_proj_mcmc.Rd
man/plot_catch_fit_mcmc.Rd
man/plot_catch_fleet.Rd
man/plot_distribution.Rd
man/plot_f_mcmc.Rd
man/plot_index_mcmc.Rd
man/plot_index_mpd.Rd
man/plot_pairs_mcmc.Rd
man/plot_param_stats_mcmc.Rd
man/plot_priors_posts_mcmc.Rd
man/plot_q_mcmc.Rd
man/plot_rdevs_mcmc.Rd
man/plot_recr_grid_mcmc.Rd
man/plot_recr_mcmc.Rd
man/plot_recr_mpd.Rd
man/plot_ref_points.Rd
man/plot_ref_points_dist_mcmc.Rd
man/plot_selex_gear_mcmc.Rd
man/plot_selex_mcmc.Rd
man/plot_selex_mpd.Rd
man/plot_sr_mcmc.Rd
man/plot_traces_mcmc.Rd
man/plot_ts_mcmc.Rd
man/plot_tv_selex_mpd.Rd
man/plot_vuln_mcmc.Rd
man/rdata.file.Rd
man/read.list.Rd
man/read_control_file.Rd
man/read_data_file.Rd
man/read_mcmc.Rd
man/read_par_file.Rd
man/read_projection_file.Rd
man/read_psv.Rd
man/read_report_file.Rd
man/rename_gear_iscam.Rd
man/rep.file.Rd
man/replace_gear_name_and_save.Rd
man/replace_gear_names.Rd
man/retro.dir.Rd
man/run_iscam.Rd
man/run_multiple_iscam.Rd
man/run_retro.Rd
man/sel_param_est_mpd_table.Rd
man/set_dirs.Rd
man/set_gear_language.Rd
man/simplify_names.Rd
man/standardize_comps.Rd
man/strip_static_params.Rd
man/table_bio_depl.Rd
man/table_catch.Rd
man/table_catch_area.Rd
man/table_catch_fleet.Rd
man/table_catch_fleets.Rd
man/table_decision.Rd
man/table_decisions.Rd
man/table_growth_params.Rd
man/table_index_values.Rd
man/table_iscam_param_desc.Rd
man/table_param_est_mcmc.Rd
man/table_param_est_mpd.Rd
man/table_param_phi_mpd.Rd
man/table_param_settings.Rd
man/table_ref_points_mcmc.Rd
man/table_ref_rate.Rd
man/table_sens_param_changes.Rd
man/table_sens_q.Rd
man/table_ts_values_mcmc.Rd
man/tex.Rd
man/tr.Rd
man/vec2df.Rd
man/write_projection_file.Rd
tests/testthat.R
tests/testthat/test-utilities.R
