Files in pbs-assess/gfranges

Groundfish Ranges

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/bioclimatic-predictions.R R/calcslope.R R/make-trend-data.R R/make-vector-data.R R/make_prediction_grid.R R/mature-biomass-est.R R/maturity.R R/plot-clusters.R R/plot-coefs.R R/plot-conditional-effects.R R/plot-gamm-coefs.R R/plot-maps.R R/plot-mountains.R R/plot-vocc-interaction.R R/quiver.R R/spatiotemporal-data.R R/survey-data-processing.R R/theme_black.R R/vocc-gradient.R R/vocc-modelling-scratch.R R/vocc.R README.md analysis/SOPO/1-render-maturity.R analysis/SOPO/1-trawl-split-by-maturity.Rmd analysis/SOPO/2-render-models.R analysis/SOPO/2-trawl-depth-only-model.Rmd analysis/SOPO/2-trawl-no-covs-model.Rmd analysis/SOPO/3-pool-indices.R analysis/SOPO/4-plot-index.R analysis/SOPO/get-all-trawl-spp.R analysis/SOPO/hbll.R analysis/SOPO/make-grids.R analysis/SOPO/trawl-stats.R analysis/VOCC/0-packages.R analysis/VOCC/1-render-maturity.R analysis/VOCC/1-split-biomass-by-maturity.Rmd analysis/VOCC/2-biomass-depth-only-model.Rmd analysis/VOCC/2-biomass-depth-only-model2.Rmd analysis/VOCC/2-check-biomass-grads.Rmd analysis/VOCC/2-improve-biomass-models.Rmd analysis/VOCC/2-render-biomass-model.R analysis/VOCC/3-render-biotic-vocc.R analysis/VOCC/3-vocc-dist.Rmd analysis/VOCC/4-fishing-trend.Rmd analysis/VOCC/4-pool-biotic-vocc.R analysis/VOCC/4-prep-var-vocc.R analysis/VOCC/5-add-null.R analysis/VOCC/5-life-history-stats.R analysis/VOCC/6-vocc-regression.R analysis/VOCC/7-chopsticks.R analysis/VOCC/7-coef-plots.R analysis/VOCC/8-behav-functions.R analysis/VOCC/8-define-clusters.R analysis/VOCC/BACI/4-vocc-BACI-multiyear.Rmd analysis/VOCC/BACI/4-vocc-BACI-render.Rmd

analysis/VOCC/BACI/basic_spatial.cpp

analysis/VOCC/BACI/basic_spatial_re.cpp

analysis/VOCC/BACI/basic_spatial_re_fix_sigma.cpp

analysis/VOCC/BACI/gamm-draft.R analysis/VOCC/BACI/render-matches.R analysis/VOCC/BACI/vocc-modelling-fix-sigma.R analysis/VOCC/BACI/vocc-modelling.R analysis/VOCC/bioclimatic/3-bioclimatic-trends.Rmd analysis/VOCC/bioclimatic/3-climate-model-temp-or-do.Rmd analysis/VOCC/bioclimatic/3-climate-models-fixed-depth.Rmd analysis/VOCC/bioclimatic/4-dvocc-bioclimatic.R analysis/VOCC/bioclimatic/4-pool-lag-estimates.R analysis/VOCC/bioclimatic/4-vocc-bioclimatic.R analysis/VOCC/bioclimatic/4-vocc-bioclimatic.Rmd analysis/VOCC/biomass-climate-models.Rmd analysis/VOCC/biomass-trends.Rmd analysis/VOCC/fixed-var-response-plots.Rmd analysis/VOCC/get-combined-covariates.R analysis/VOCC/get-data.R analysis/VOCC/get-fishing-intensity.R analysis/VOCC/get-footprint.R analysis/VOCC/get-substrate.R analysis/VOCC/maturity-test.R analysis/VOCC/old-code/1-biomass-do-models-fixed-both.Rmd analysis/VOCC/old-code/1-biomass-do-models-fixed.Rmd analysis/VOCC/old-code/1-biomass-do-models.Rmd analysis/VOCC/old-code/1-biomass-temp-models-fixed-both.Rmd analysis/VOCC/old-code/1-biomass-temp-models-fixed.Rmd analysis/VOCC/old-code/1-biomass-temp-models.Rmd analysis/VOCC/old-code/3-fixed-var-response-hist.Rmd analysis/VOCC/old-code/3-variable-response-plots.Rmd analysis/VOCC/old-code/4-vocc-BACI.Rmd analysis/VOCC/old-code/4-vocc-biotic.R analysis/VOCC/old-code/4-vocc-by-spp.Rmd analysis/VOCC/old-code/5-vcc-functions.R analysis/VOCC/old-code/dist-vocc-do-1n3.Rmd analysis/VOCC/old-code/dist-vocc-temp-do-4.Rmd analysis/VOCC/old-code/dist-vocc-temp-do-asym-1n3.Rmd analysis/VOCC/old-code/dist-vocc-temp-do-asym-4.Rmd analysis/VOCC/old-code/dist-vocc-temp.R analysis/VOCC/old-code/dist-vocc-temp.Rmd analysis/VOCC/old-code/dist-vocc.Rmd analysis/VOCC/old-code/gradient-vocc.R analysis/VOCC/old-code/vocc-regression-vel.R analysis/VOCC/old-code/vocc-regression-with-extra-plots.R analysis/VOCC/plot-depth.R analysis/VOCC/plot-depths-selected.R analysis/VOCC/render-biomass-trends.R analysis/VOCC/render-scrambled-years.R analysis/VOCC/render-thresholds.R analysis/VOCC/tests/vocc-test.R analysis/VOCC/vocc-example.Rmd analysis/VOCC/vocc-regression-functions.R

analysis/VOCC/vocc_regression.cpp

analysis/misc/get-data-ambre.R analysis/misc/get-skates.R analysis/misc/halibut-south-outside.Rmd analysis/misc/longspine-map.R analysis/misc/yelloweye-south-outside.Rmd analysis/sand-lance/biomass-density-model.Rmd analysis/sand-lance/occupancy-model.Rmd

analysis/tmb-sensor-explore/.gitignore

analysis/tmb-sensor-explore/1-get-SST-data.R analysis/tmb-sensor-explore/1-get-all-sensor-dat.R analysis/tmb-sensor-explore/1-get-sensor-dat.R analysis/tmb-sensor-explore/2-fit-exploration.Rmd analysis/tmb-sensor-explore/2-fit-temperature.Rmd analysis/tmb-sensor-explore/3-fit-do-salinity.Rmd analysis/tmb-sensor-explore/3-fit-do.Rmd analysis/tmb-sensor-explore/4-mountain-rw-examples.Rmd analysis/tmb-sensor-explore/5-vcc.R analysis/tmb-sensor-explore/6-model-checks.R analysis/tmb-sensor-explore/boosted-reg-model.R analysis/tmb-sensor-explore/climate-predictions.R analysis/tmb-sensor-explore/extract_ROMS.R

gfranges.Rproj

literature/apa-annotated-bibliograph-inline.csl

literature/apa_annotated_20180708.csl

literature/other-range-shift-notes.md

literature/pbs-rangeshifts-edit.bib

literature/range-shift-lit-review-notes.Rmd man/add_colours.Rd man/add_missing_depths.Rd man/align_legend.Rd man/bioclim_by_year.Rd man/bioclim_multi_year.Rd man/calcslope.Rd man/chopstick_slopes.Rd man/coef_scatterplot.Rd man/collapse_outliers.Rd man/dist_based_vocc.Rd man/dotplot_error.Rd man/effect_plot.Rd man/firstup.Rd man/fixed_density.Rd man/geom_quiver.Rd man/get_optimal_value.Rd man/get_quadratic_roots.Rd man/interaction_df.Rd man/interp_survey_bathymetry.Rd man/make_gradient_brick.Rd man/make_raster_brick.Rd man/make_trend_data.Rd man/make_vector_data.Rd man/plot_chop_est.Rd man/plot_chopstick_slopes.Rd man/plot_clusters.Rd man/plot_coefs.Rd man/plot_effect_continuous.Rd man/plot_facet_map.Rd man/plot_fuzzy_chopsticks.Rd man/plot_gradient_vocc.Rd man/plot_mat_ogive.Rd man/plot_mountains.Rd man/plot_parametric.Rd man/plot_raw_chopsticks.Rd man/plot_survey_sets.Rd man/plot_vocc.Rd man/raster_slopes.Rd man/scale_predictors.Rd man/shortener.Rd man/slope_scatterplot.Rd man/spatiotemporal_grid.Rd man/split_catch_maturity.Rd man/tidy_survey_sets.Rd man/time_varying_density.Rd man/trim_vector_data.Rd man/vocc_gradient_calc.Rd

ms/ecology.csl

ms/make-figs.R ms/make-supp-figs.R ms/make-tables.R

ms/makefile

ms/refs.bib

prediction-grids/overall-grid.rds

pbs-assess/gfranges documentation built on Dec. 13, 2021, 4:50 p.m.