Files in nikolaifish/bamExtras

Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

FunctionsToAdd.R R/F_calc.r R/L2F.r R/L_calc.r R/M_Charnov.R R/M_Lorenzen.R R/M_calc.r R/ROGBP.r R/add2rdat.r R/agelenprob.r R/bam2r.r R/bamdat2mat.r R/barplot_stacked.r R/bic2lk.r R/catch_curve.r R/check_bounds.r R/color_trans.r R/comp_combine.r R/comp_complete.r R/comp_complete_bam.r R/comp_plot.r R/cor2csv.r R/data.R R/data_lim.R R/data_polate.R R/dbllgs.r R/exp_decay.r R/figs2tex.R R/find_replace.r R/geomean.r R/geomean2.r R/get_msy.r R/get_tpl_nm.r R/get_weighted_current.r R/lgs.r R/lnorm_cv.r R/lnorm_cv2sd.r R/lnorm_sd.r R/lnorm_vector_boot.r R/logit.r R/mean_noNA.r R/mse_calc.r R/plot_MCBE.R R/plot_bam.R R/plot_boot_density.R R/plot_boot_vec.R R/plot_data_timeline.R R/plot_profile.R R/pmatage.r R/random_walk.R R/run_MCBE.R R/run_bam.R R/run_proj.r R/run_proj_seq.r R/run_retro.R R/sections.r R/sel_comp.r R/sr_eq.r R/standardize_bam.r R/standardize_rdat.r R/stepwise.R R/summarize_MCBE.R R/text_legend.r R/tseries_plot.r R/vb_age.r R/vb_len.r R/vector_combine.r README.md TEST_FOLDER/data.timeline.plot.R TEST_FOLDER/plot_bam/BSR.time.plotsNK.r TEST_FOLDER/plot_bam/StockRec.plots.testargs.R TEST_FOLDER/plot_bam/_06_BAM_go.r TEST_FOLDER/plot_bam/spp-figs - 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Copy/sel/spp.sel.age.rGN.D.2007.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rGN.D.2013.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.1978.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.1984.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.1999.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.2006.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.2012.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.D.1978.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.D.1999.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.D.2007.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.rHB.D.2013.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.sBT.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.sTV.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.wgted.D.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.wgted.L.pdf TEST_FOLDER/plot_bam/spp-figs - Copy/sel/spp.sel.age.wgted.tot.pdf TEST_FOLDER/run_MCBE/runMCBE_test_args.R TEST_FOLDER/run_MCBE/run_MCBE_test.Rmd TEST_FOLDER/run_retro/run_retro_testargs.R man/F_calc.Rd man/L2F.Rd man/L_calc.Rd man/M_Charnov.Rd man/M_Lorenzen.Rd man/M_calc.Rd man/ROGBP.Rd man/add2rdat.Rd man/agelenprob.Rd man/bam2r.Rd man/bamStockMisc.Rd man/bamdat2mat.Rd man/barplot_stacked.Rd man/bic2lk.Rd man/catch_curve.Rd man/check_bounds.Rd man/color_trans.Rd man/comp_combine.Rd man/comp_complete.Rd man/comp_complete_bam.Rd man/comp_plot.Rd man/cor2csv.Rd man/data_lim.Rd man/data_polate.Rd man/dbllgs.Rd man/exp_decay.Rd man/figs2tex.Rd man/find_replace.Rd man/geomean.Rd man/geomean2.Rd man/get_msy.Rd man/get_tpl_nm.Rd man/get_weighted_current.Rd man/inputData_RedPorgy.Rd man/inputData_Tilefish.Rd man/lgs.Rd man/lnorm_cv.Rd man/lnorm_cv2sd.Rd man/lnorm_sd.Rd man/lnorm_vector_boot.Rd man/logit.Rd man/mean_noNA.Rd man/mse_calc.Rd man/plot_MCBE.Rd man/plot_bam.Rd man/plot_boot_density.Rd man/plot_boot_vec.Rd man/plot_data_timeline.Rd man/plot_profile.Rd man/pmatage.Rd man/random_walk.Rd man/rdat_AtlanticMenhaden.Rd man/rdat_BlackSeaBass.Rd man/rdat_BluelineTilefish.Rd man/rdat_Cobia.Rd man/rdat_GagGrouper.Rd man/rdat_GrayTriggerfish.Rd man/rdat_GreaterAmberjack.Rd man/rdat_RedGrouper.Rd man/rdat_RedPorgy.Rd man/rdat_RedSnapper.Rd man/rdat_SnowyGrouper.Rd man/rdat_SpanishMackerel.Rd man/rdat_Tilefish.Rd man/rdat_VermilionSnapper.Rd man/run_MCBE.Rd man/run_bam.Rd man/run_proj.Rd man/run_proj_seq.Rd man/run_retro.Rd man/sections.Rd man/sel_comp.Rd man/sr_eq.Rd man/standardize_bam.Rd man/standardize_rdat.Rd man/stepwise.Rd man/summarize_MCBE.Rd man/text_legend.Rd man/tseries_plot.Rd man/vb_age.Rd man/vb_len.Rd man/vector_combine.Rd update.package.bamExtras.r vignettes/intro.Rmd