Package index • PREVAIL

All functions

PREVAIL_locations: Country and Territory ISO3 Codes

UN_WPP_fertility: UN World Population Prospects 2024: Fertility Rates

UN_WPP_migration: UN World Population Prospects 2024: Net Migration Rate

UN_WPP_mortality: UN World Population Prospects 2024: Crude Death Rates

UN_WPP_population_female: UN World Population Prospects 2024: Female Population

UN_WPP_population_total: UN World Population Prospects 2024: Total Population

VIMC_vaccination_sia: Supplementary Immunization Activities (SIA) Coverage Estimates

WHO_disease_reports: WHO Global Reported Cases of Vaccine-Preventable Diseases (1980–2023)

WHO_vaccination_routine: WHO Routine Infant Immunization Coverage (WUENIC)

WHO_vaccination_schedule: WHO Reported Vaccination Schedules

WHO_vaccination_sia: WHO Supplementary Immunization Activities (SIA) Vaccination Data

age_breaks_to_labels(): Convert Age Break String to Age Group Labels

aggregate_contact_matrix(): aggregate_contact_matrix

aggregate_model_output_by_time(): Aggregate Model Output by Time Units (State-Specific Aggregation)

calc_aging_and_repro(): Calculate Aging Rates, Reproductive Parameters, and Maternal Protection

calculate_current_susceptibility(): Calculate Final Susceptibility and Recovered States

combine_ggplot(): Combine Two ggplot2 Plots with Consistent Style, Geom, and Axis Expansion

compare_weighted_inputs(): Compare Two Inputs Using Population Weights or Sum

contact_matricies: Social Contact Matrices from Prem et al. (2017)

custom_data_process_wrapper(): custom_data_process_wrapper

data_load_process_wrapper(): data_load_process_wrapper

demographic_check(): Compare Model Population to Population Reference Estimates

disease_parameters: Disease Natural History Parameters

fit_transmission_model(): Fit Transmission Model Using PMCMC

generate_domain_from_map(): Generate a Valid Parameter Domain Around MAP Estimates

get_WHO_region(): Assign WHO Region to ISO3 Country Codes

get_income_group(): Assign World Bank Income Group from ISO3 Country Codes

prepare_future_data(): Prepare Future Scenario Parameters for Transmission Model

rds_names: Names of Data Objects Included in the PREVAIL Package

reformat_cases(): Reformat Custom Case Data for Model Input

reformat_contact_matrix(): Reformat Data.frame into a Contact Matrix

reformat_demographic_data(): Reformat Demographic Data to Model Structure

reformat_parameters(): Reformat Parameter Table for Model Input

reformat_vaccination(): Reformat Custom Vaccination Data for Model Input

reformat_vaccination_schedule(): Reformat Vaccination Schedule Data

run_model(): Run Dust Model Simulation

run_model_unpack_results(): Run and Unpack Dust Model Simulation Results

scenario_compare(): Compare Two Transmission Scenarios

summary_plots(): Generate Summary Plots and Susceptibility Profiles

unpack_dust2(): Unpack Dust Model State Data

vaccination_pre1980: Historical Vaccination Introduction and Coverage (Pre-1980)

vaccine_parameters: Vaccine Efficacy and Duration Parameters