Files in njhenry/covidemr
Tools for Mapping COVID Excess Mortality
.gitattributes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/covariate_diagnostic_functions.R
R/covariate_prep_functions.R
R/ita_covariate_prep_functions.R
R/ita_data_prep_functions.R
R/model_functions.R
R/postestimation_functions.R
R/predictive_validity_functions.R
R/spatial_data_functions.R
R/viz_functions.R
README.md
conda_create_R_environment.sh
covidemr.Rproj
environment.yml
exec/00_download_data.sh
exec/01_create_ita_prov_list.R
exec/02_ita_data_prep.R
exec/02a_input_data_diagnostics.R
exec/03_ita_estimation_run.R
exec/04_visualization.R
exec/04b_predictive_validity_metrics.R
exec/04c_compile_pv_metrics.R
exec/TEST_ita_remake_preds.R
exec/cluster_R_exec.sh
exec/launch_model_viz.sh
exec/launch_oos_pv.sh
exec/launch_test_runs.sh
exec/viz/create_map_labels.R
exec/viz/map_covariates.R
exec/viz/map_excess_mort_weekly.R
inst/extdata/config.yaml
inst/extdata/province_labels.csv
inst/extdata/region_labels.csv
man/aggregate_data_and_draws.Rd
man/aggregate_summarize_excess.Rd
man/array_split.Rd
man/assign_seasonality_ids.Rd
man/backfill_input_data.Rd
man/build_adjacency_matrix.Rd
man/calculate_coverage.Rd
man/calculate_excess_time_series.Rd
man/calculate_excess_time_series_by_group.Rd
man/calculate_rmse_rse.Rd
man/check_covar_validity.Rd
man/create_age_groups.Rd
man/create_template_dt.Rd
man/extend_covar_time_series.Rd
man/find_glm_map_parameter_estimates.Rd
man/generate_stwa_draws.Rd
man/get_covar_prep_function.Rd
man/get_covar_vif.Rd
man/get_fourier_seasonality_fit.Rd
man/hello.Rd
man/icar_precision_from_adjacency.Rd
man/index_populated_grid_cells.Rd
man/ita_prepare_covar_elevation.Rd
man/ita_prepare_covar_hc_access.Rd
man/ita_prepare_covar_pop_density.Rd
man/ita_prepare_covar_socserv.Rd
man/ita_prepare_covar_tax_brackets.Rd
man/ita_prepare_covar_tax_income.Rd
man/ita_prepare_covar_temperature.Rd
man/ita_prepare_covar_tfr.Rd
man/ita_prepare_covar_unemp.Rd
man/ita_prepare_covar_year_cov.Rd
man/ita_prepare_covariate.Rd
man/ita_prepare_deaths_all_years.Rd
man/ita_prepare_deaths_single_year.Rd
man/ita_prepare_pop.Rd
man/ita_read_istat_csv.Rd
man/ita_temperature_query_api.Rd
man/italian_cities_dt.Rd
man/load_format_pop_raster.Rd
man/load_format_spatial_polys.Rd
man/map_ita_choropleth.Rd
man/map_ita_choropleth_region.Rd
man/normalize_adfun.Rd
man/rescale_prepped_covariates.Rd
man/rmvnorm_prec.Rd
man/run_sparsity_algorithm.Rd
man/setup_run_tmb.Rd
man/summarize_draws.Rd
man/week_id_from_date.Rd
man/weekly_harmonic_freq.Rd
src/mort_stwa.cpp
