Man pages for njhenry/covidemr
Tools for Mapping COVID Excess Mortality
| aggregate_data_and_draws | Aggregate data and draws |
| aggregate_summarize_excess | Aggregate and summarize excess mortality estimates |
| array_split | Split a matrix into N chunks by row |
| assign_seasonality_ids | Assign seasonality grouping IDs |
| backfill_input_data | Backfill missing historical data |
| build_adjacency_matrix | Build adjacency matrix |
| calculate_coverage | Calculate coverage across predictive draws |
| calculate_excess_time_series | Calculate excess mortality time series for a single... |
| calculate_excess_time_series_by_group | Calculate time series of excess mortality across multiple... |
| calculate_rmse_rse | Calculate RMSE and RSE for predictive estimates |
| check_covar_validity | Validate prepared covariate data |
| create_age_groups | Create age group categories |
| create_template_dt | Create template data.table to store all observed data |
| extend_covar_time_series | Extend a covariate time series forward |
| find_glm_map_parameter_estimates | Get Maximum a Priori (MAP) parameter estimates |
| generate_stwa_draws | Create post-estimation predictive draws |
| get_covar_prep_function | Pull a specific prep function for an Italy covariate |
| get_covar_vif | Get Variance Inflation Factors for a set of covariates |
| get_fourier_seasonality_fit | Generate weekly fluctuations in mortality based on fit... |
| hello | Hello, World! |
| icar_precision_from_adjacency | Generate an ICAR precision matrix based on an adjacency... |
| index_populated_grid_cells | Get populated grid cells by location |
| italian_cities_dt | Get largest Italian cities |
| ita_prepare_covar_elevation | Prepare covariate: Elevation |
| ita_prepare_covar_hc_access | Prepare covariate: access to healthcare facility |
| ita_prepare_covariate | Prepare an Italy covariate for modeling |
| ita_prepare_covar_pop_density | Prepare covariate: population density |
| ita_prepare_covar_socserv | Prepare social services covariate |
| ita_prepare_covar_tax_brackets | Prepare covariate: proportion of households with income under... |
| ita_prepare_covar_tax_income | Prepare covariate: mean taxable income across all households |
| ita_prepare_covar_temperature | Prepare covariate: weekly temperature |
| ita_prepare_covar_tfr | Prepare TFR covariate |
| ita_prepare_covar_unemp | Prepare unemployment covariate |
| ita_prepare_covar_year_cov | Prepare year covariate |
| ita_prepare_deaths_all_years | Prepare death data for Italy |
| ita_prepare_deaths_single_year | Prepare a single year of death data for Italy |
| ita_prepare_pop | Prepare population data for Italy |
| ita_read_istat_csv | Read CSV downloaded from iStat |
| ita_temperature_query_api | Load and cache daily temperature data from API |
| load_format_pop_raster | Load and format population raster |
| load_format_spatial_polys | Load and format spatial polygons for modeling |
| map_ita_choropleth | Make a choropleth map of Italian provinces |
| map_ita_choropleth_region | Make a choropleth map of Italian REGIONS |
| normalize_adfun | Run TMB normalization |
| rescale_prepped_covariates | Rescale observed covariates |
| rmvnorm_prec | Take multivariate normal draws given a mean vector and... |
| run_sparsity_algorithm | Run TMB precision matrix sparsity algorithm |
| setup_run_tmb | Set up and run TMB |
| summarize_draws | Summarize predictive draws |
| week_id_from_date | Get week ID from date |
| weekly_harmonic_freq | Get weekly harmonic frequency |
