├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── describe-issue.md │ └── feature_request.md └── workflows │ ├── R-CMD-check.yaml │ ├── rhub.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.note ├── NAMESPACE ├── NEWS.md ├── R ├── cAIC.R ├── data.R ├── family.R ├── fit.R ├── internal.R ├── make_dsem_ram.R ├── make_eof_ram.R ├── make_sem_ram.R ├── mesh.R ├── methods.R ├── predict.R ├── project.R ├── sfnetwork.R └── utility.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data-raw ├── download_sea_ice.R ├── format_condition_and_density.R ├── format_red_snapper.R ├── format_salmon_returns.R └── mcf210023-sup-0001-tables1-s24 -- ST 13-16 Tot ret (bioma) 52-15.csv ├── data ├── alaska_sponge_coral_fish.rda ├── bering_sea.rda ├── bering_sea_capelin_forecasts.rda ├── bering_sea_pollock_ages.rda ├── bering_sea_pollock_vast.rda ├── condition_and_density.rda ├── red_grouper_diet.rda ├── red_snapper.rda ├── red_snapper_shapefile.rda ├── salmon_returns.rda └── sea_ice.rda ├── header.md ├── inst ├── CITATION └── stream_network │ ├── East_Fork_Lewis_basin.dbf │ ├── East_Fork_Lewis_basin.prj │ ├── East_Fork_Lewis_basin.shp │ └── East_Fork_Lewis_basin.shx ├── man ├── GetResponse.tinyVAST.Rd ├── add_mesh_covariates.Rd ├── add_predictions.Rd ├── alaska_sponge_coral_fish.Rd ├── bering_sea.Rd ├── bering_sea_capelin_forecasts.Rd ├── bering_sea_pollock_ages.Rd ├── bering_sea_pollock_vast.Rd ├── cAIC.Rd ├── classify_variables.Rd ├── condition_and_density.Rd ├── conditional_gmrf.Rd ├── deviance_explained.Rd ├── families.Rd ├── figures │ └── logo.png ├── get_data.tinyVAST.Rd ├── integrate_output.Rd ├── logLik.tinyVAST.Rd ├── make_dsem_ram.Rd ├── make_eof_ram.Rd ├── make_sem_ram.Rd ├── parse_path.Rd ├── predict.tinyVAST.Rd ├── print.tinyVAST.Rd ├── project.Rd ├── red_grouper_diet.Rd ├── red_snapper.Rd ├── red_snapper_shapefile.Rd ├── reexports.Rd ├── reload_model.Rd ├── residuals.tinyVAST.Rd ├── rmvnorm_prec.Rd ├── rotate_pca.Rd ├── salmon_returns.Rd ├── sample_variable.Rd ├── sea_ice.Rd ├── sfnetwork_evaluator.Rd ├── sfnetwork_mesh.Rd ├── simulate.tinyVAST.Rd ├── simulate_sfnetwork.Rd ├── spatial_cor.Rd ├── summary.tinyVAST.Rd ├── term_covariance.Rd ├── tinyVAST.Rd ├── tinyVASTcontrol.Rd └── vcov.tinyVAST.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon.png │ ├── favicon-96x96.png │ ├── favicon.ico │ ├── favicon.svg │ ├── site.webmanifest │ ├── web-app-manifest-192x192.png │ └── web-app-manifest-512x512.png ├── scratch ├── SAR_sfpolygon.R ├── Thorson_2024_GEB.R ├── Upload_to_CRAN.R ├── VAST.Rmd ├── age_composition_expansion.Rmd ├── barrier-mgcv.R ├── build_pkgdown_website.R ├── build_r-devel_in_WSL.R ├── compare_PESC.R ├── condition.Rmd ├── crossvalidation.R ├── dbinom_robust_mathcheck.R ├── develop_barrier_spde.R ├── develop_kappa_covariates.R ├── develop_project.R ├── empirical_orthogonal_functions.Rmd ├── fit.R ├── icon.png ├── network_precision_check.R ├── 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