Files in James-Thorson/FishStatsUtils
Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox
DESCRIPTION
LICENSE
NAMESPACE
R/FishStatsUtils.R
R/Prepare_XXXX_Extrapolation_Data_Fn.R
R/Print_Message.R
R/amend_output.R
R/calc_cov.R
R/calculate_knot_areas.R
R/calculate_proportion.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/fit_model.R
R/get_latest_version.R
R/inla.barrier.fem.copy.R
R/latlon_to_SpatialPolygons.R
R/load_example.R
R/make_covariates.R
R/make_extrapolation_info.R
R/make_kmeans.R
R/make_map_info.R
R/make_mesh.R
R/make_settings.R
R/make_spatial_info.R
R/marginaleffects.R
R/match_strata_fn.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/rotate_factors.R
R/sample_variable.R
R/simulate_data.R
R/strip_units.R
R/zzz.R
README.md
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
inst/extdata/AI_POP/Kmeans-250.RData
inst/extdata/AI_POP/Record.RData
inst/extdata/AI_POP/opt.RData
inst/extdata/EBS_pollock/Kmeans_knots-100.RData
inst/extdata/EBS_pollock/Record.RData
inst/extdata/EBS_pollock/opt.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/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/FishStatsUtils.Rd
man/GOA_pcod_covariate_example.Rd
man/Geostat_Sim.Rd
man/PlotMap_Fn.Rd
man/Rerun_Fn.Rd
man/Vessel_Fn.Rd
man/amend_output.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/combine_extrapolation_info.Rd
man/combine_lists.Rd
man/convert_shapefile.Rd
man/convert_version_name.Rd
man/fit_model.Rd
man/format_covariates.Rd
man/get_latest_version.Rd
man/goa_traits.Rd
man/load_example.Rd
man/make_covariates.Rd
man/make_extrapolation_info.Rd
man/make_kmeans.Rd
man/make_map_info.Rd
man/make_mesh.Rd
man/make_settings.Rd
man/make_spatial_info.Rd
man/map_hypervariance.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_factors.Rd
man/plot_index.Rd
man/plot_legend.Rd
man/plot_loadings.Rd
man/plot_maps.Rd
man/plot_overdispersion.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_extrapolation_info.Rd
man/print.make_spatial_info.Rd
man/project_coordinates.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/summarize_covariance.Rd
man/summary.fit_model.Rd
