|
admin_covariates
|
Covariates at admin unit 1 level. |
|
age_structure
|
Countries' age structure |
|
average_up()
|
Aggregate FOI predictions at 1/6 degree resolutions to adim unit level |
|
calculate_wgt_cor()
|
Calculate weighted Pearson correlation coefficient |
|
create_lookup_tables()
|
Create look up tables for burden and R0 calculation |
|
create_parameter_list()
|
Create a list of user-defined parameters |
|
exp_max_algorithm()
|
Fit a random forest using an EM algorithm |
|
fitted_sero_cell_to_adm()
|
Modify predictions of serology data points at 1/6 degree resolution |
|
fit_ranger_RF()
|
Fit a random forest model |
|
foi_data
|
Force of infection estimates and covariates at admin unit 1. |
|
full_routine_bootstrap()
|
Pre-process and fit a random forest model to a sample of FOI data |
|
generic_scatter_plot()
|
Plot observations vs predictions |
|
get_sat_area_wgts()
|
Calculate case weights for admin unit 1 level pseudo absences |
|
grid_and_boot()
|
Generate a block bootstrapped sample of the original FOI data. |
|
loop()
|
Parallel computation wrapper |
|
make_ranger_predictions()
|
Generate predictions from a Ranger model fit |
|
map_preprocess()
|
Preprocess data for ggplot map |
|
post_processing_burden()
|
Post-process the output of the burden calculation |
|
predictor_rank
|
Selected predictors. |
|
preprocess_adm_data()
|
Pre-process the original admin unit level FOI dataset |
|
preprocess_pxl_data()
|
Pre-process the 1/6 degree resolution FOI dataset |
|
pre_process_vaccine_lookup_table()
|
Pre-process the vaccine impact look up table |
|
quick_raster_map()
|
Plot and save a raster map |
|
R0_to_prop_cases_averted_lookup_1
|
Look up table of vaccine impact on mild cases (R0 assumption 1). |
|
R0_to_prop_cases_averted_lookup_2
|
Look up table of vaccine impact on mild cases (R0 assumption 2). |
|
R0_to_prop_hosp_averted_lookup_1
|
Look up table of vaccine impact on hospitalized cases (R0 assumption 1). |
|
R0_to_prop_hosp_averted_lookup_2
|
Look up table of vaccine impact on hospitalized cases (R0 assumption 2). |
|
R0_to_prop_infections_averted_lookup_1
|
Look up table of vaccine impact on infections (R0 assumption 1). |
|
R0_to_prop_infections_averted_lookup_2
|
Look up table of vaccine impact on infections (R0 assumption 2). |
|
set_wgts_to_sero_cells()
|
Calculate case weights for serology 1/6 degree resolution cells |
|
wrapper_to_replicate_R0_and_burden()
|
Look up the impact of a transmission-reducing intervention |