Files in Blue-Matter/SAMtool
Stock Assessment Methods Toolkit
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/rchk.yml
.github/workflows/test-coverage.yaml
.github/workflows/valgrind.yml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/Ancillary_Indicators.R
R/HCRs.R
R/Misc_fun.R
R/RCM2.R
R/RCM2MOM.R
R/RCM_assess.R
R/RCM_data.R
R/RCM_est.R
R/RCM_int.R
R/RCM_rmd.R
R/SAMtool-package.R
R/assess_DD.R
R/assess_SCA.R
R/assess_SCA_ext.R
R/assess_SP.R
R/assess_SSS.R
R/assess_VPA.R
R/assess_cDD.R
R/assess_shortcut.R
R/define_S4_class_RCModel.R
R/define_S4_class_assess_RCMdata.R
R/define_S4_class_profile.R
R/define_S4_class_project.R
R/define_S4_class_retro.R
R/define_S4_generic_RCM.R
R/define_S4_generic_posterior.R
R/define_S4_generic_simulate.R
R/diagnostic.R
R/document_data.R
R/interim_MP.R
R/report_DD_TMB.R
R/report_SCA.R
R/report_SP.R
R/report_SSS.R
R/report_VPA.R
R/report_auxiliary.R
R/report_cDD.R
R/report_spict.R
R/retrospective_AM.R
R/rmd_report.R
R/z_MPs.R
R/zzz.R
README.Rmd
README.md
SAMtool.Rproj
_pkgdown.yml
data-raw/extra/Data_files/Data_ORH7A.csv
data-raw/extra/Data_files/GulfMenhaden_Data.csv
data-raw/extra/Data_files/Yellow_striped_MPerf.csv
data-raw/extra/Data_files/dat.rda
data-raw/extra/GoM_cod/cod_RCM.R
data-raw/extra/GoM_cod/cod_SRA.rds
data-raw/extra/GoM_cod/cod_args.rds
data-raw/extra/GoM_cod/cod_args_MRAMP.rds
data-raw/extra/japanese_seabass/Japanese_Seabas.OM
data-raw/extra/japanese_seabass/Japanese_Seabas_data_new_indices.csv
data-raw/extra/japanese_seabass/MERA_TokyoBayData.csv
data-raw/extra/japanese_seabass/dat.rda
data-raw/extra/pcod/pcod_RCM.R
data-raw/extra/snapper/OM.rda
data-raw/extra/snapper/datS.rda
data-raw/extra/tiger_flathead/OM.rda
data-raw/extra/tiger_flathead/Tiger_flathead_data.csv
data-raw/extra/tiger_flathead/dat.rda
data-raw/extra/useful_check_code.R
data-raw/extra/valgrind_make_asesss.R
data-raw/extra/valgrind_run_check.R
data-raw/extra/yelloweye_rockfish/IYE_RCM.R
data-raw/extra/yelloweye_rockfish/IYE_SRA.rds
data-raw/extra/yelloweye_rockfish/IYE_data.rds
data-raw/extra/yelloweye_rockfish/IYE_ret.rds
data-raw/make_pcod.R
data-raw/pcod-data-5ABCD.rds
data-raw/swordfish.R
data-raw/swordfish.csv
data-raw/vignette_SAMtool.R
data/pcod.rda
data/swordfish.rda
inst/include/DD.hpp
inst/include/RCM.hpp
inst/include/SCA.hpp
inst/include/SP.hpp
inst/include/VPA.hpp
inst/include/cDD.hpp
inst/include/functions.hpp
inst/include/ns/ns_DD.hpp
inst/include/ns/ns_RCM.hpp
inst/include/ns/ns_SCA.hpp
inst/include/ns/ns_SP.hpp
inst/include/ns/ns_VPA.hpp
inst/include/ns/ns_cDD.hpp
man/Assessment-class.Rd
man/DD_TMB.Rd
man/HCR_FB.Rd
man/HCR_MSY.Rd
man/HCR_escapement.Rd
man/HCR_fixedF.Rd
man/HCR_ramp.Rd
man/HCR_segment.Rd
man/HCRlin.Rd
man/Model-based-MP.Rd
man/PRBcalc.Rd
man/Probs.Rd
man/RCM.Rd
man/RCM2MOM.Rd
man/RCM_assess.Rd
man/RCMdata-class.Rd
man/RCModel-class.Rd
man/SAMtool-package.Rd
man/SCA.Rd
man/SCA_CAL.Rd
man/SCA_DDM.Rd
man/SCA_RWM.Rd
man/SP.Rd
man/SP_production.Rd
man/SSS.Rd
man/Shortcut.Rd
man/TAC_MSY.Rd
man/VPA.Rd
man/cDD.Rd
man/compare_models.Rd
man/diagnostic.Rd
man/figures/logo.png
man/getinds.Rd
man/mahplot.Rd
man/make_MP.Rd
man/pcod.Rd
man/plot.Assessment.Rd
man/plot.RCModel.Rd
man/plot.prof.Rd
man/plot.retro.Rd
man/plot_SR.Rd
man/plot_betavar.Rd
man/plot_composition.Rd
man/plot_crosscorr.Rd
man/plot_lognormalvar.Rd
man/plot_residuals.Rd
man/plot_steepness.Rd
man/plot_timeseries.Rd
man/posterior.Rd
man/prelim_AM.Rd
man/prof-class.Rd
man/profile.Rd
man/project-class.Rd
man/projection.Rd
man/retro-class.Rd
man/retrospective.Rd
man/retrospective_AM.Rd
man/sim-class.Rd
man/simulate.Rd
man/summary.Assessment.Rd
man/swordfish.Rd
man/userguide.Rd
src/SAMtool.cpp
tests/test-Hist.R
tests/test-MSE.R
tests/test-RCM.R
tests/test-projection.R
