Files in ecohealthalliance/hotspots2
Analysis of the Hotspots dataset on disease emergence
.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/clip_at_sd.R
R/fit_brts_to_events.R
R/join_predictors.R
R/multibrt.R
R/partial_dependence_plot_factors.R
R/partial_dependence_plot_truncated.R
R/partial_dependence_plots.R
R/prettyquick.R
R/quickmap.R
R/raster_plot.R
R/relative_influence_plots.R
R/sample_bsm_events.R
R/sample_cv_events.R
R/sample_kfold_events.R
R/sample_loocv_events.R
R/sum_presences_and_absences.R
R/template_raster.R
R/utils.R
R/winsorize.R
README.md
data-raw/README.md
data-raw/consolidate.R
data-raw/drivers_orig.R
data-raw/earthenv.R
data-raw/eid_metadata.R
data-raw/eid_shapefiles.R
data-raw/gens.R
data-raw/mammal_species_richness.R
data-raw/pubcrawler.R
data/change.RData
data/continents.RData
data/country_outlines.RData
data/decadal.RData
data/drivers.RData
data/drivers_full.RData
data/eid_metadata.RData
data/event_coverage.RData
data/predictions.RData
data/template_df.RData
hotspots2.Rproj
inst/out/additional_figures/correlations.pdf
inst/out/additional_figures/map1.png
inst/out/additional_figures/map2.png
inst/out/additional_figures/map_bsm_response.pdf
inst/out/additional_figures/map_bsm_response.png
inst/out/additional_figures/map_bsm_response_labeled1.pdf
inst/out/additional_figures/map_bsm_response_labeled1.png
inst/out/additional_figures/map_bsm_response_labeled2.pdf
inst/out/additional_figures/map_bsm_response_labeled2.png
inst/out/additional_figures/map_bsm_weight_pop.pdf
inst/out/additional_figures/map_bsm_weight_pop.png
inst/out/additional_figures/map_bsm_weight_pop_large.pdf
inst/out/additional_figures/map_bsm_weight_pop_large.png
inst/out/additional_figures/map_bsm_weight_pubs.pdf
inst/out/additional_figures/map_bsm_weight_pubs.png
inst/out/additional_figures/pubcrawler_hires.pdf
inst/out/additional_figures/pubcrawler_hires.png
inst/out/additional_figures/pubcrawler_hires_quantvar.pdf
inst/out/additional_figures/pubcrawler_hires_quantvar.png
inst/out/additional_figures/pubcrawler_hires_truncated.pdf
inst/out/additional_figures/pubcrawler_hires_truncated.png
inst/out/additional_figures/pubs_fit.pdf
inst/out/additional_figures/pubs_fit.png
inst/out/additional_figures/pubs_jones.pdf
inst/out/additional_figures/pubs_jones.png
inst/out/additional_figures/scatterplotmatrix.pdf
inst/out/additional_figures/scatterplotmatrix.png
inst/out/additional_figures/weighted_land_area_absences.pdf
inst/out/additional_figures/weighted_land_area_presences.pdf
inst/out/additional_figures/weighted_pubs_fit_absences.pdf
inst/out/additional_figures/weighted_pubs_fit_presences.pdf
inst/out/additional_figures/wildlife_zoonoses_post-70_unweighted.pdf
inst/out/additional_figures/wildlife_zoonoses_post-70_unweighted_log.pdf
inst/out/additional_figures/wildlife_zoonoses_pre-70_unweighted.pdf
inst/out/additional_figures/wildlife_zoonoses_pre-70_unweighted_log.pdf
inst/out/additional_figures/wildlife_zoonoses_unweighted.pdf
inst/out/additional_figures/wildlife_zoonoses_unweighted_log.pdf
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent.pdf
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent.png
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent_centered.pdf
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent_centered.png
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent_faceted.pdf
inst/out/asl_2050_continent/asl_2050_continent_livestock_by_continent_faceted.png
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_box_scatter.pdf
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_box_scatter.png
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_boxplot.pdf
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_boxplot.png
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_scatterplot.pdf
inst/out/asl_2050_continent/asl_2050_continent_partial_dependence_scatterplot.png
inst/out/asl_2050_continent/asl_2050_continent_relative_influence.pdf
inst/out/asl_2050_continent/asl_2050_continent_relative_influence.png
inst/out/asl_2050_continent/info
inst/out/asl_2050_continent/interactions.csv
inst/out/asl_2050_continent/percent_deviance_explained
inst/out/asl_2050_continent/summary
inst/out/bsm_1000_iter/bsm_1000_iter_partial_dependence_hist.pdf
inst/out/bsm_1000_iter/bsm_1000_iter_partial_dependence_hist.png
inst/out/bsm_1000_iter/bsm_1000_iter_partial_dependence_hist_truncated.pdf
inst/out/bsm_1000_iter/bsm_1000_iter_partial_dependence_hist_truncated.png
inst/out/bsm_1000_iter/bsm_1000_iter_relative_influence.pdf
inst/out/bsm_1000_iter/bsm_1000_iter_relative_influence.png
inst/out/bsm_1000_iter/cv_summary_flattened
inst/out/bsm_1000_iter/info
inst/out/bsm_1000_iter/interactions.csv
inst/out/bsm_1000_iter/percent_deviance_explained
inst/out/bsm_1000_iter/summary
inst/out/bsm_1000_noweight/bsm_1000_noweight_partial_dependence_hist.pdf
inst/out/bsm_1000_noweight/bsm_1000_noweight_partial_dependence_hist.png
inst/out/bsm_1000_noweight/bsm_1000_noweight_partial_dependence_hist_truncated.pdf
inst/out/bsm_1000_noweight/bsm_1000_noweight_partial_dependence_hist_truncated.png
inst/out/bsm_1000_noweight/bsm_1000_noweight_relative_influence.pdf
inst/out/bsm_1000_noweight/bsm_1000_noweight_relative_influence.png
inst/out/bsm_1000_noweight/info
inst/out/bsm_1000_noweight/interactions.csv
inst/out/bsm_1000_noweight/percent_deviance_explained
inst/out/bsm_1000_noweight/summary
inst/out/data for yingying 2018-01-30/bsm_response.asc
inst/out/data for yingying 2018-01-30/bsm_response.csv
inst/out/data for yingying 2018-01-30/bsm_response.tif
inst/out/eidrc_maps/eidrc_bsm_response_inferno.pdf
inst/out/eidrc_maps/eidrc_bsm_response_inferno.png
inst/out/eidrc_maps/eidrc_bsm_response_spectral.pdf
inst/out/eidrc_maps/eidrc_bsm_response_spectral.png
inst/out/eidrc_maps/eidrc_bsm_response_viridis.pdf
inst/out/eidrc_maps/eidrc_bsm_response_viridis.png
inst/out/export_for_yasha_2018-03-05/export_readme.md
inst/out/kfold_10x100_iter/cv_summary_flattened
inst/out/kfold_10x100_iter/cv_summary_unflattened
inst/out/kfold_10x100_iter/cv_with_noweight_summary_flattened
inst/out/kfold_10x100_iter/cv_with_noweight_summary_unflattened
inst/out/kfold_10x100_iter/info
inst/out/kfold_10x100_iter/kfold_10x100_iter_partial_dependence_hist.pdf
inst/out/kfold_10x100_iter/kfold_10x100_iter_partial_dependence_hist.png
inst/out/kfold_10x100_iter/kfold_10x100_iter_relative_influence.pdf
inst/out/kfold_10x100_iter/kfold_10x100_iter_relative_influence.png
inst/out/kfold_10x100_iter/summary_interactions
inst/out/kfold_noweight_10x100_iter/cv_summary_flattened
inst/out/kfold_noweight_10x100_iter/cv_summary_unflattened
inst/out/kfold_noweight_10x100_iter/info
inst/out/kfold_noweight_10x100_iter/kfold_noweight_10x100_iter_partial_dependence_hist.pdf
inst/out/kfold_noweight_10x100_iter/kfold_noweight_10x100_iter_partial_dependence_hist.png
inst/out/kfold_noweight_10x100_iter/kfold_noweight_10x100_iter_relative_influence.pdf
inst/out/kfold_noweight_10x100_iter/kfold_noweight_10x100_iter_relative_influence.png
inst/out/kfold_noweight_10x100_iter/summary_interactions
inst/out/loocvm_10_iter/info
inst/out/loocvm_10_iter/loocvm_10_iter_partial_dependence_hist.pdf
inst/out/loocvm_10_iter/loocvm_10_iter_partial_dependence_hist.png
inst/out/loocvm_10_iter/loocvm_10_iter_partial_dependence_hist_truncated.pdf
inst/out/loocvm_10_iter/loocvm_10_iter_partial_dependence_hist_truncated.png
inst/out/loocvm_10_iter/loocvm_10_iter_relative_influence.pdf
inst/out/loocvm_10_iter/loocvm_10_iter_relative_influence.png
inst/out/loocvm_10_iter/summary_interactions
inst/out/loocvm_noweight_10_iter/info
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_partial_dependence_hist.pdf
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_partial_dependence_hist.png
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_partial_dependence_hist_truncated.pdf
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_partial_dependence_hist_truncated.png
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_relative_influence.pdf
inst/out/loocvm_noweight_10_iter/loocvm_noweight_10_iter_relative_influence.png
inst/out/maps_2019-07-18/hotspots_inferno_blue.pdf
inst/out/maps_2019-07-18/hotspots_inferno_blue.png
inst/out/maps_2019-07-18/hotspots_inferno_clear.pdf
inst/out/maps_2019-07-18/hotspots_inferno_clear.png
inst/out/maps_2019-07-18/hotspots_spectral_blue.pdf
inst/out/maps_2019-07-18/hotspots_spectral_blue.png
inst/out/maps_2019-07-18/hotspots_spectral_clear.pdf
inst/out/maps_2019-07-18/hotspots_spectral_clear.png
inst/out/maps_2019-07-18/hotspots_viridis_blue.pdf
inst/out/maps_2019-07-18/hotspots_viridis_blue.png
inst/out/maps_2019-07-18/hotspots_viridis_clear.pdf
inst/out/maps_2019-07-18/hotspots_viridis_clear.png
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_inferno.pdf
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_inferno.png
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_spectral.pdf
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_spectral.png
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_viridis.pdf
inst/out/maps_2019-11-06/armenia-azerbaijan-georgia-map_viridis.png
inst/out/ncd-eid-link/hs2_country.csv
inst/out/ncd-eid-link/hs2_grid.csv
inst/out/ncd-eid-link/hs2_region.csv
inst/out/predictions.csv
inst/out/predictions_summed_to_country.csv
inst/out/raster/README.md
inst/out/raster/bsm_response.tif
inst/out/raster/bsm_weight_pop.tif
inst/out/raster/bsm_weight_pubs.tif
inst/out/raster/hotspots2_clipped.tif
inst/out/raster/hotspots2_clipped_hires.tif
inst/out/raster/hotspots2_predictions.csv
inst/out/subset_maps/Africa_reweighted.pdf
inst/out/subset_maps/Africa_reweighted.png
inst/out/subset_maps/Armenia, Azerbaijan, Georgia_reweighted.pdf
inst/out/subset_maps/Armenia, Azerbaijan, Georgia_reweighted.png
inst/out/subset_maps/Armenia_reweighted.pdf
inst/out/subset_maps/Armenia_reweighted.png
inst/out/subset_maps/Azerbaijan_reweighted.pdf
inst/out/subset_maps/Azerbaijan_reweighted.png
inst/out/subset_maps/Burkina Faso_reweighted.pdf
inst/out/subset_maps/Burkina Faso_reweighted.png
inst/out/subset_maps/Egypt_reweighted.pdf
inst/out/subset_maps/Egypt_reweighted.png
inst/out/subset_maps/Ethiopia_reweighted.pdf
inst/out/subset_maps/Ethiopia_reweighted.png
inst/out/subset_maps/Georgia_reweighted.pdf
inst/out/subset_maps/Georgia_reweighted.png
inst/out/subset_maps/Nigeria_reweighted.pdf
inst/out/subset_maps/Nigeria_reweighted.png
inst/out/subset_maps/Uganda_reweighted.pdf
inst/out/subset_maps/Uganda_reweighted.png
inst/scratch/asl_2050_continent.R
inst/scripts/asl_2050_continent_workflow.R
inst/scripts/bsm_noweight_workflow.R
inst/scripts/bsm_noweight_workflow_pubs_fit.R
inst/scripts/bsm_slow_workflow.R
inst/scripts/bsm_workflow.R
inst/scripts/compare_bsm_slow.R
inst/scripts/figures_etc/additional_figures.R
inst/scripts/figures_etc/compare_jones_pubs.R
inst/scripts/figures_etc/compare_pubs_layers.R
inst/scripts/figures_etc/country_level_maps.R
inst/scripts/figures_etc/country_summary_for_epicore.R
inst/scripts/figures_etc/event_maps.R
inst/scripts/figures_etc/export_data_for_yingying_2018-01-30.R
inst/scripts/figures_etc/export_for_ncd_eid_link.R
inst/scripts/figures_etc/export_for_nicholas_ray_2018-08-13.R
inst/scripts/figures_etc/export_for_yasha_2018-03-02.R
inst/scripts/figures_etc/export_kml.R
inst/scripts/figures_etc/figures_for_belmont.R
inst/scripts/figures_etc/figures_for_eidrc.R
inst/scripts/figures_etc/map_cropped_at_lonlat.R
inst/scripts/figures_etc/map_predictions.R
inst/scripts/figures_etc/pubcrawler_plots.R
inst/scripts/figures_etc/sink_info.R
inst/scripts/figures_etc/variable_maps.R
inst/scripts/kfold_evaluate_flattened.R
inst/scripts/kfold_evaluate_unflattened.R
inst/scripts/kfold_evaluate_with_noweight_flattened.R
inst/scripts/kfold_evaluate_with_noweight_unflattened.R
inst/scripts/kfold_noweight_evaluate_flattened.R
inst/scripts/kfold_noweight_evaluate_unflattened.R
inst/scripts/kfold_noweight_workflow.R
inst/scripts/kfold_workflow.R
inst/scripts/loocv_evaluate.R
inst/scripts/loocv_evaluate_with_noweight_events.R
inst/scripts/loocv_noweight_evaluate.R
inst/scripts/loocv_noweight_workflow.R
inst/scripts/loocv_workflow.R
inst/scripts/pubs_models/1_import_all_pubs_layers.R
inst/scripts/pubs_models/2_define_functions.R
inst/scripts/pubs_models/3_run_models.R
inst/scripts/single_model.R
inst/scripts/test_workflow.R
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
