Files in DanOvando/sraplus
Run sraplus Assessments
.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/RcppExports.R
R/cod.R
R/data.R
R/diagnose-sraplus.R
R/find_ancestors.R
R/fit-prior-regressions.R
R/fit-sraplus.R
R/fit_tmb.R
R/format-driors.R
R/get-posterior.R
R/get_prior_posterior.R
R/get_tmb_model.R
R/get_traits.R
R/plot-driors.R
R/plot-prior-posterior.R
R/plot-sraplus.R
R/search_species.R
R/sraplus-package.R
R/sraplus_simulator.R
R/stack-stan.R
R/summarize-sraplus.R
R/theme-sraplus.R
R/utils-pipe.R
R/zzz.R
README.Rmd
README.md
README_files/figure-gfm/c-msy-3-1.png
README_files/figure-gfm/cpue-fit-1-1.png
README_files/figure-gfm/fmi-sar-1-1.png
README_files/figure-gfm/fmi-sar-2-1.png
README_files/figure-gfm/sim-index-1-1.png
README_files/figure-gfm/unnamed-chunk-10-1.png
README_files/figure-gfm/unnamed-chunk-11-1.png
README_files/figure-gfm/unnamed-chunk-11-2.png
README_files/figure-gfm/unnamed-chunk-11-3.png
README_files/figure-gfm/unnamed-chunk-13-1.png
README_files/figure-gfm/unnamed-chunk-14-1.png
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README_files/figure-gfm/unnamed-chunk-6-1.png
README_files/figure-gfm/unnamed-chunk-9-1.png
_pkgdown.yml
data-raw/.gitignore
data-raw/DATASET.R
data-raw/Exvessel Price Database.csv
data-raw/FMI data extract by stock for Ray 2018-11-05.xlsx
data-raw/OverlapTable2.csv
data-raw/RAM FMI stocks and taxonomic groupings.xlsx
data-raw/RAM vs FMI.csv
data-raw/RAM-FMI linkages for DO 2019-09-16.xlsx
data-raw/RamStocksWithID2.csv
data-raw/country-to-fao-area.csv
data-raw/fao-to-bell-region.csv
data-raw/fmi_scinames.rds
data-raw/thorson_2012_data.csv
data/Data_Effort_CPUE_forRH.csv
data/FishBase_and_RAM.rda
data/FlounderTimeseries.xlsx
data/catch_b_model.rda
data/class_fit.rda
data/cluster_fit.rda
data/cod.rda
data/fao_taxa.rda
data/fmi.rda
data/fmi_models.rda
data/init_state_model.rda
data/ram_fmi.rda
data/sar.rda
data/sar_models.rda
data/sraplus-template.xlsx
data/ssb0msy_to_ssb0.rda
docs/404.html
docs/LICENSE-text.html
docs/_config.yml
docs/articles/index.html
docs/articles/prior-tuning.html
docs/articles/prior-tuning_files/figure-html/driors-1.png
docs/articles/prior-tuning_files/figure-html/tuned-fit-1.png
docs/articles/prior-tuning_files/figure-html/unnamed-chunk-2-1.png
docs/articles/prior-tuning_files/figure-html/untuned-fit-1.png
docs/articles/prior-tuning_files/header-attrs-2.11/header-attrs.js
docs/articles/sraplus.html
docs/articles/sraplus_files/figure-html/c-msy-3-1.png
docs/articles/sraplus_files/figure-html/cpue-fit-1-1.png
docs/articles/sraplus_files/figure-html/fmi-sar-1-1.png
docs/articles/sraplus_files/figure-html/fmi-sar-2-1.png
docs/articles/sraplus_files/figure-html/sim-index-1-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-10-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-10-2.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-11-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-11-2.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-11-3.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-12-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-13-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-14-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-15-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-16-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-17-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-18-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-6-1.png
docs/articles/sraplus_files/figure-html/unnamed-chunk-9-1.png
docs/articles/sraplus_files/header-attrs-2.11/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/cod.html
docs/reference/diagnose_sraplus.html
docs/reference/figures/README-c-msy-3-1.png
docs/reference/figures/README-cpue-fit-1-1.png
docs/reference/figures/README-fmi-sar-1-1.png
docs/reference/figures/README-fmi-sar-2-1.png
docs/reference/figures/README-sim-index-1-1.png
docs/reference/figures/README-unnamed-chunk-10-1.png
docs/reference/figures/README-unnamed-chunk-11-1.png
docs/reference/figures/README-unnamed-chunk-11-2.png
docs/reference/figures/README-unnamed-chunk-11-3.png
docs/reference/figures/README-unnamed-chunk-13-1.png
docs/reference/figures/README-unnamed-chunk-14-1.png
docs/reference/figures/README-unnamed-chunk-16-1.png
docs/reference/figures/README-unnamed-chunk-17-1.png
docs/reference/figures/README-unnamed-chunk-18-1.png
docs/reference/figures/README-unnamed-chunk-19-1.png
docs/reference/figures/README-unnamed-chunk-6-1.png
docs/reference/figures/README-unnamed-chunk-9-1.png
docs/reference/fit_prior_regressions.html
docs/reference/fit_sraplus.html
docs/reference/format_driors.html
docs/reference/get_posterior.html
docs/reference/get_prior_posterior.html
docs/reference/get_tmb_model.html
docs/reference/index.html
docs/reference/pipe.html
docs/reference/plot_driors.html
docs/reference/plot_prior_posterior.html
docs/reference/plot_sraplus.html
docs/reference/sraplus-package.html
docs/reference/sraplus_simulator.html
docs/reference/stack_stan.html
docs/reference/summarize_sralpus.html
docs/reference/theme_sraplus.html
man/FishBase_and_RAM.Rd
man/cod.Rd
man/diagnose_sraplus.Rd
man/figures/README-c-msy-3-1.png
man/figures/README-cpue-fit-1-1.png
man/figures/README-fmi-sar-1-1.png
man/figures/README-fmi-sar-2-1.png
man/figures/README-sim-index-1-1.png
man/figures/README-unnamed-chunk-10-1.png
man/figures/README-unnamed-chunk-11-1.png
man/figures/README-unnamed-chunk-11-2.png
man/figures/README-unnamed-chunk-11-3.png
man/figures/README-unnamed-chunk-13-1.png
man/figures/README-unnamed-chunk-14-1.png
man/figures/README-unnamed-chunk-16-1.png
man/figures/README-unnamed-chunk-17-1.png
man/figures/README-unnamed-chunk-18-1.png
man/figures/README-unnamed-chunk-19-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-9-1.png
man/find_ancestors.Rd
man/fit_prior_regressions.Rd
man/fit_sraplus.Rd
man/fit_tmb.Rd
man/format_driors.Rd
man/get_posterior.Rd
man/get_prior_posterior.Rd
man/get_tmb_model.Rd
man/get_traits.Rd
man/pipe.Rd
man/plot_driors.Rd
man/plot_prior_posterior.Rd
man/plot_sraplus.Rd
man/search_species.Rd
man/sraplus-package.Rd
man/sraplus_simulator.Rd
man/stack_stan.Rd
man/summarize_sralpus.Rd
man/theme_sraplus.Rd
simple_test.R
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/TMB/compile.R
src/TMB/sraplus_TMBExports.cpp
src/TMB/sraplus_tmb.hpp
src/sraplus.cpp
test_sraplus.R
tests/testthat.R
tests/testthat/test-sir.R
tests/testthat/test-stan.R
vignettes/.gitignore
vignettes/sraplus.Rmd
