Files in James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model

.Rbuildignore

.github/workflows/R-CMD-check.yml

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/Prepare_XXXX_Extrapolation_Data_Fn.R R/Print_Message.R R/TMBAIC.R R/VAST.R R/amend_output.R R/apply_epsilon.R R/calc_cov.R R/calculate_knot_areas.R R/calculate_proportion.R R/check_fit.R R/combine_extrapolation_info.R R/combine_lists.R R/convert_shapefile.R R/convert_version_name.R R/data.R R/deprecated.R R/effects.R R/fit_model.R R/fit_tmb.R R/get_latest_version.R R/inla.barrier.fem.copy.R R/latlon_to_SpatialPolygons.R R/list_parameters.R R/load_example.R R/make_covariates.R R/make_data.R R/make_extrapolation_info.R R/make_kmeans.R R/make_map.R R/make_map_info.R R/make_mesh.R R/make_model.R R/make_parameters.R R/make_settings.R R/make_spatial_info.R R/marginaleffects.R R/match_strata_fn.R R/oneStepPredict_deltaModel.R R/plot_anisotropy.R R/plot_biomass_index.R R/plot_clusters.R R/plot_data.R R/plot_dharma.R R/plot_factors.R R/plot_index.R R/plot_legend.R R/plot_loadings.R R/plot_maps.r R/plot_overdispersion.R R/plot_quantile_residuals.R R/plot_range_edge.R R/plot_range_index.R R/plot_residual_semivariance.R R/plot_results.R R/plot_similarity.R R/plot_timeseries.R R/plot_variable.R R/project_coordinates.R R/project_model.R R/reload_model.R R/rotate_factors.R R/sample_variable.R R/simulate_data.R R/strip_units.R R/zzz.R README.md

VAST.Rproj

data/AI_pacific_ocean_perch.rda

data/BC_pacific_cod_example.rda

data/BFISH_MHI.rda

data/EBS_pollock_data.rda

data/GOA_arrowtooth_condition_and_density.rda

data/GOA_pacific_cod.rda

data/GOA_pcod_covariate_example.rda

data/GOA_walleye_pollock.rda

data/GSL_american_plaice.rda

data/NWA_yellowtail_seasons.rda

data/PESC_example_red_grouper.rda

data/WCGBTS_Canary_example.rda

data/WCGHL_grid.rda

data/WC_triennial_yelloweye.rda

data/acoustic_and_trawl.rda

data/aleutian_islands_grid.rda

data/arrowtooth_trends.rda

data/bc_coast_grid.rda

data/bering_sea_slope_grid.rda

data/california_current_grid.rda

data/chatham_rise_grid.rda

data/chatham_rise_hake.rda

data/chukchi_sea_grid.rda

data/comp_expansion_example.rda

data/condition_and_density_example.rda

data/eastern_bering_sea_grid.rda

data/five_species_ordination_example.rda

data/georges_bank_haddock_fall.rda

data/georges_bank_haddock_spring.rda

data/goa_mice_example.rda

data/goa_traits.rda

data/gulf_of_alaska_grid.rda

data/gulf_of_mexico_grid.rda

data/gulf_of_st_lawrence_grid.rda

data/habcam_grid.rda

data/iceland_cod.rda

data/multimodal_red_snapper_example.rda

data/north_sea_IBTS_sample_locations.rda

data/northern_bering_sea_grid.rda

data/northwest_atlantic_grid.csv

data/northwest_atlantic_grid.rda

data/pollock_cohorts.rda

data/south_africa_grid.rda

data/south_africa_westcoast_jacopever.rda

data/st_matthews_island_grid.rda

data/stream_network_eel_example.rda

docs/index.html

docs/static/badge.png

docs/static/badge_external_active.png

docs/static/check.png

docs/static/greybadge.png

docs/static/greycheck.png

docs/static/icons8-checkmark-24-external-active.png

docs/static/icons8-email-send-24.png

docs/static/icons8-github-32.png

docs/static/icons8-pdf-50.png

docs/static/noaa-fisheries-rgb-2line-horizontal-small.png

docs/static/simple.css

inst/CITATION

inst/executables/VAST_v10_0_0.cpp

inst/executables/VAST_v11_0_0.cpp

inst/executables/VAST_v12_0_0.cpp

inst/executables/VAST_v13_0_0.cpp

inst/executables/VAST_v13_1_0.cpp

inst/executables/VAST_v14_0_0.cpp

inst/executables/VAST_v14_0_1.cpp

inst/executables/VAST_v8_0_0.cpp

inst/executables/VAST_v8_1_0.cpp

inst/executables/VAST_v8_2_0.cpp

inst/executables/VAST_v8_3_0.cpp

inst/executables/VAST_v8_4_0.cpp

inst/executables/VAST_v8_5_0.cpp

inst/executables/VAST_v8_6_0.cpp

inst/executables/VAST_v9_0_0.cpp

inst/executables/VAST_v9_1_0.cpp

inst/executables/VAST_v9_2_0.cpp

inst/executables/VAST_v9_3_0.cpp

inst/executables/VAST_v9_4_0.cpp

inst/extdata/AI_POP/Kmeans-250.RData

inst/extdata/AI_POP/Record.RData

inst/extdata/AI_POP/opt.RData

inst/extdata/Condition_and_density/saved_estimates.RData

inst/extdata/EBS_3species/Data_Geostat.RData

inst/extdata/EBS_3species/Kmeans-50.RData

inst/extdata/EBS_3species/Record.RData

inst/extdata/EBS_3species/opt.RData

inst/extdata/EBS_3species/parhat.RData

inst/extdata/EBS_5species/Data_Geostat.RData

inst/extdata/EBS_5species/Kmeans-100.RData

inst/extdata/EBS_5species/Record.RData

inst/extdata/EBS_5species/opt.RData

inst/extdata/EBS_5species/parhat.RData

inst/extdata/EBS_pollock/Kmeans_knots-100.RData

inst/extdata/EBS_pollock/Record.RData

inst/extdata/EBS_pollock/opt.RData

inst/extdata/EOF/Kmeans_extrapolation-2000.RData

inst/extdata/EOF/Kmeans_knots-50.RData

inst/extdata/EOF/parameter_estimates.RData

inst/extdata/GOA_MICE_example/Kmeans-50.RData

inst/extdata/GOA_MICE_example/saved_estimates.RData

inst/extdata/GOA_MICE_example/settings.RData

inst/extdata/Lingcod_comp_expansion/Data_Geostat.RData

inst/extdata/Lingcod_comp_expansion/Kmeans-50.RData

inst/extdata/Lingcod_comp_expansion/Record.RData

inst/extdata/Lingcod_comp_expansion/opt.RData

inst/extdata/Spatially_varying_coefficient/Data.RData

inst/extdata/Spatially_varying_coefficient/Kmeans-100.RData

inst/extdata/Spatially_varying_coefficient/saved_estimates.RData

inst/extdata/Spatially_varying_coefficient/settings.RData

inst/extdata/Stream_network/parameter_estimates.RData

inst/extdata/Stream_network/settings.RData

inst/extdata/WCGBTS_canary/Kmeans-100.RData

inst/extdata/WCGBTS_canary/Record.RData

inst/extdata/WCGBTS_canary/opt.RData

inst/extdata/chatham_rise_hake/Kmeans-250.RData

inst/extdata/chatham_rise_hake/Record.RData

inst/extdata/chatham_rise_hake/opt.RData

inst/region_shapefiles/AI/AI.dbf

inst/region_shapefiles/AI/AI.prj

inst/region_shapefiles/AI/AI.shp

inst/region_shapefiles/AI/AI.shx

inst/region_shapefiles/ATL-IBTS-Q1/Shapefile.dbf

inst/region_shapefiles/ATL-IBTS-Q1/Shapefile.prj

inst/region_shapefiles/ATL-IBTS-Q1/Shapefile.shp

inst/region_shapefiles/ATL-IBTS-Q1/Shapefile.shx

inst/region_shapefiles/ATL-IBTS-Q4/Shapefile.dbf

inst/region_shapefiles/ATL-IBTS-Q4/Shapefile.prj

inst/region_shapefiles/ATL-IBTS-Q4/Shapefile.shp

inst/region_shapefiles/ATL-IBTS-Q4/Shapefile.shx

inst/region_shapefiles/BITS/Shapefile.dbf

inst/region_shapefiles/BITS/Shapefile.prj

inst/region_shapefiles/BITS/Shapefile.shp

inst/region_shapefiles/BITS/Shapefile.shx

inst/region_shapefiles/BTS-VIIa/Shapefile.dbf

inst/region_shapefiles/BTS-VIIa/Shapefile.prj

inst/region_shapefiles/BTS-VIIa/Shapefile.shp

inst/region_shapefiles/BTS-VIIa/Shapefile.shx

inst/region_shapefiles/BTS/Shapefile.dbf

inst/region_shapefiles/BTS/Shapefile.prj

inst/region_shapefiles/BTS/Shapefile.shp

inst/region_shapefiles/BTS/Shapefile.shx

inst/region_shapefiles/CALCOFI-IMECOCAL_SUMMER/Shapefile.dbf

inst/region_shapefiles/CALCOFI-IMECOCAL_SUMMER/Shapefile.prj

inst/region_shapefiles/CALCOFI-IMECOCAL_SUMMER/Shapefile.shp

inst/region_shapefiles/CALCOFI-IMECOCAL_SUMMER/Shapefile.shx

inst/region_shapefiles/CALCOFI-IMECOCAL_WINTER-SPRING/Shapefile.dbf

inst/region_shapefiles/CALCOFI-IMECOCAL_WINTER-SPRING/Shapefile.prj

inst/region_shapefiles/CALCOFI-IMECOCAL_WINTER-SPRING/Shapefile.shp

inst/region_shapefiles/CALCOFI-IMECOCAL_WINTER-SPRING/Shapefile.shx

inst/region_shapefiles/CALCOFI_WINTER-SPRING/Shapefile.dbf

inst/region_shapefiles/CALCOFI_WINTER-SPRING/Shapefile.prj

inst/region_shapefiles/CALCOFI_WINTER-SPRING/Shapefile.shp

inst/region_shapefiles/CALCOFI_WINTER-SPRING/Shapefile.shx

inst/region_shapefiles/Chukchi/Chukchi.dbf

inst/region_shapefiles/Chukchi/Chukchi.prj

inst/region_shapefiles/Chukchi/Chukchi.shp

inst/region_shapefiles/Chukchi/Chukchi.shx

inst/region_shapefiles/EBSshelf/EBSshelf.dbf

inst/region_shapefiles/EBSshelf/EBSshelf.prj

inst/region_shapefiles/EBSshelf/EBSshelf.shp

inst/region_shapefiles/EBSshelf/EBSshelf.shx

inst/region_shapefiles/EBSslope/EBSslope.dbf

inst/region_shapefiles/EBSslope/EBSslope.prj

inst/region_shapefiles/EBSslope/EBSslope.shp

inst/region_shapefiles/EBSslope/EBSslope.shx

inst/region_shapefiles/EVHOE/Shapefile.dbf

inst/region_shapefiles/EVHOE/Shapefile.prj

inst/region_shapefiles/EVHOE/Shapefile.shp

inst/region_shapefiles/EVHOE/Shapefile.shx

inst/region_shapefiles/GOA/GOA.dbf

inst/region_shapefiles/GOA/GOA.prj

inst/region_shapefiles/GOA/GOA.shp

inst/region_shapefiles/GOA/GOA.shx

inst/region_shapefiles/IE-IGFS/Shapefile.dbf

inst/region_shapefiles/IE-IGFS/Shapefile.prj

inst/region_shapefiles/IE-IGFS/Shapefile.shp

inst/region_shapefiles/IE-IGFS/Shapefile.shx

inst/region_shapefiles/IMECOCAL_WINTER-SPRING/Shapefile.dbf

inst/region_shapefiles/IMECOCAL_WINTER-SPRING/Shapefile.prj

inst/region_shapefiles/IMECOCAL_WINTER-SPRING/Shapefile.shp

inst/region_shapefiles/IMECOCAL_WINTER-SPRING/Shapefile.shx

inst/region_shapefiles/NBS/NBS.dbf

inst/region_shapefiles/NBS/NBS.prj

inst/region_shapefiles/NBS/NBS.shp

inst/region_shapefiles/NBS/NBS.shx

inst/region_shapefiles/NIGFS/Shapefile.dbf

inst/region_shapefiles/NIGFS/Shapefile.prj

inst/region_shapefiles/NIGFS/Shapefile.shp

inst/region_shapefiles/NIGFS/Shapefile.shx

inst/region_shapefiles/NS_IBTS/Shapefile.dbf

inst/region_shapefiles/NS_IBTS/Shapefile.prj

inst/region_shapefiles/NS_IBTS/Shapefile.shp

inst/region_shapefiles/NS_IBTS/Shapefile.shx

inst/region_shapefiles/PT-IBTS/Shapefile.dbf

inst/region_shapefiles/PT-IBTS/Shapefile.prj

inst/region_shapefiles/PT-IBTS/Shapefile.shp

inst/region_shapefiles/PT-IBTS/Shapefile.shx

inst/region_shapefiles/ROCKFISH_RECRUITMENT_COASTWIDE/Shapefile.dbf

inst/region_shapefiles/ROCKFISH_RECRUITMENT_COASTWIDE/Shapefile.prj

inst/region_shapefiles/ROCKFISH_RECRUITMENT_COASTWIDE/Shapefile.shp

inst/region_shapefiles/ROCKFISH_RECRUITMENT_COASTWIDE/Shapefile.shx

inst/region_shapefiles/ROCKFISH_RECRUITMENT_CORE/Shapefile.dbf

inst/region_shapefiles/ROCKFISH_RECRUITMENT_CORE/Shapefile.prj

inst/region_shapefiles/ROCKFISH_RECRUITMENT_CORE/Shapefile.shp

inst/region_shapefiles/ROCKFISH_RECRUITMENT_CORE/Shapefile.shx

inst/region_shapefiles/SP-ARSA/Shapefile.dbf

inst/region_shapefiles/SP-ARSA/Shapefile.prj

inst/region_shapefiles/SP-ARSA/Shapefile.shp

inst/region_shapefiles/SP-ARSA/Shapefile.shx

inst/region_shapefiles/SP-NORTH/Shapefile.dbf

inst/region_shapefiles/SP-NORTH/Shapefile.prj

inst/region_shapefiles/SP-NORTH/Shapefile.shp

inst/region_shapefiles/SP-NORTH/Shapefile.shx

inst/region_shapefiles/SP-PORC/Shapefile.dbf

inst/region_shapefiles/SP-PORC/Shapefile.prj

inst/region_shapefiles/SP-PORC/Shapefile.shp

inst/region_shapefiles/SP-PORC/Shapefile.shx

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.cpg

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.dbf

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.prj

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.sbn

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.sbx

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.shp

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.shp.xml

inst/region_shapefiles/WCGBTS/WCGBTS_Grid_v2008_Albers.shx

man/Build_TMB_Fn.Rd man/Calc_Anisotropic_Mesh.Rd man/Calc_Polygon_Areas_and_Polygons_Fn.Rd man/Coherence.Rd man/Convert_LL_to_EastNorth_Fn.Rd man/Convert_LL_to_UTM_Fn.Rd man/Crossvalidate_Fn.Rd man/Data_Fn.Rd man/Effect.fit_model.Rd man/GOA_pcod_covariate_example.Rd man/Geostat_Sim.Rd man/Param_Fn.Rd man/PlotMap_Fn.Rd man/Plot_Overdispersion.Rd man/Plot_factors.Rd man/Rerun_Fn.Rd man/Summarize_Covariance.Rd man/TMBAIC.Rd man/VAST.Rd man/amend_output.Rd man/apply_epsilon.Rd man/arrowtooth_trends.Rd man/bilinear_interp.Rd man/calc_coherence.Rd man/calc_cov.Rd man/calc_synchrony.Rd man/calculate_knot_areas.Rd man/calculate_proportion.Rd man/check_fit.Rd man/combine_extrapolation_info.Rd man/combine_lists.Rd man/convert_shapefile.Rd man/convert_version_name.Rd man/fit_model.Rd man/fit_tmb.Rd man/format_covariates.Rd man/get_latest_version.Rd man/goa_traits.Rd man/list_parameters.Rd man/load_example.Rd man/make_covariates.Rd man/make_data.Rd man/make_extrapolation_info.Rd man/make_kmeans.Rd man/make_map.Rd man/make_map_info.Rd man/make_mesh.Rd man/make_model.Rd man/make_parameters.Rd man/make_settings.Rd man/make_spatial_info.Rd man/map_hypervariance.Rd man/oneStepPredict_deltaModel.Rd man/plot.fit_model.Rd man/plot.make_extrapolation_info.Rd man/plot.make_spatial_info.Rd man/plot_anisotropy.Rd man/plot_biomass_index.Rd man/plot_clusters.Rd man/plot_cov.Rd man/plot_data.Rd man/plot_dharma.Rd man/plot_encounter_diagnostic.Rd man/plot_index.Rd man/plot_legend.Rd man/plot_loadings.Rd man/plot_maps.Rd man/plot_quantile_diagnostic.Rd man/plot_quantile_residuals.Rd man/plot_range_edge.Rd man/plot_range_index.Rd man/plot_residual_semivariance.Rd man/plot_residuals.Rd man/plot_results.Rd man/plot_similarity.Rd man/plot_timeseries.Rd man/plot_variable.Rd man/pollock_cohorts.Rd man/predict.fit_model.Rd man/print.fit_model.Rd man/print.make_data.Rd man/print.make_extrapolation_info.Rd man/print.make_model.Rd man/print.make_spatial_info.Rd man/project_coordinates.Rd man/project_model.Rd man/reload_model.Rd man/rotate_factors.Rd man/sample_variable.Rd man/simulate_data.Rd man/smallPlot.Rd man/stream_network_eel_example.Rd man/strip_units.Rd man/summary.fit_model.Rd

manual/NEWS.docx

manual/NEWS.pdf

manual/VAST_Species_Distribution_Modeling_Workflow.png

manual/VAST_model_structure.docx

tests/testthat/testthat-problems.rds

vignettes/VAST.Rmd

James-Thorson/VAST documentation built on Feb. 9, 2025, 9:05 a.m.

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James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model

Files in James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model

R Package Documentation

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James-Thorson/VAST Vector-Autoregressive Spatio-Temporal (VAST) Model

Files in James-Thorson/VAST Vector-Autoregressive Spatio-Temporal (VAST) Model

R Package Documentation

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We want your feedback!

James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model

Files in James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model