Reference

Description
comoparams	R Utility Tool to Extract, Process and Structure Philippines-specific Datasets for Use in CoMo Consortium Model
Utility functions
ph_gdrive_files()	Get Department of Health COVID-19 Data Drop Google Drive specific directory information
Pull data
ph_get_fields()	Pull Philippines data fields information from the publicly available Department of Health COVID-19 Data Drop
ph_get_cases()	Pull Philippines data on cases information from the publicly available Department of Health COVID-19 Data Drop
ph_get_tests()	Pull Philippines data on testing aggregates from the publicly available Department of Health COVID-19 Data Drop
ph_get_daily()	Pull Philippines data on daily facilities status from the publicly available Department of Health COVID-19 Data Drop
ph_get_psa2015_pop()	Get Philippines population estimates for 2015 and projections for 2016-2025 based on the results of the Philippines 2015 POPCEN
ph_get_wpp2019_pop()	Get Philippines population estimates or projections by 5-year age groups given a year or range of years from the World Population Prospects 2019
ph_get_wpp2019_births()	Get Philippines age-specific number of births estimates or projections by 5-year periods given a year or range of years from the World Population Prospects 2019
ph_get_wpp2019_deaths()	Get Philippines number of deaths estimates or projections by 5-year periods given a year or range of years from the World Population Prospects 2019
Calculate values
ph_calculate_cases()	Calculate daily cases, daily deaths and daily recoveries from Philippines COVID-19 Data Drop
ph_calculate_rates()	Calculate infection fatality rate (IFR), infection hospitalisation rate, and hospitalisation fatality rate (HFR) from Philippines data
ph_calculate_pdeath()	Calculate probability of dying when hospitalised
ph_calculate_nus()	Duration of hospitalised infection
Set parameters
ph_set_cases()	Set Philippines-specific CoMo model simulation parameters for COVID-19 cases
ph_set_severe()	Set Philippines-specific CoMo model simulation parameters for severity of cases and mortality
ph_set_population()	Set Philippines-specific CoMo model simulation parameters for population
ph_set_general()	Set Philippines-specific CoMo model simulation parameters for general and area factors
ph_set_virus()	Set Philippines-specific CoMo model simulation parameters for virus parameters
ph_set_hospital()	Set Philippines-specific CoMo model simulation parameters for hospitalisation parameters
ph_set_lockdown()	Set Philippines-specific CoMo model simulation lockdown intervention parameters
ph_set_isolation()	Set Philippines-specific CoMo model simulation self-isolation intervention parameters
ph_set_distancing()	Set Philippines-specific CoMo model simulation social distancing intervention parameters
ph_set_handwashing()	Set Philippines-specific CoMo model simulation handwashing intervention parameters
ph_set_work()	Set Philippines-specific CoMo model simulation work from home intervention parameters
ph_set_school()	Set Philippines-specific CoMo model simulation schools closure intervention parameters
ph_set_cocoon()	Set Philippines-specific CoMo model simulation for shielding the elderly intervention parameters
ph_set_travel()	Set Philippines-specific CoMo model simulation travel ban intervention parameters
ph_set_quarantine()	Set Philippines-specific CoMo model simulation voluntary home quarantine intervention parameters
ph_set_vaccination()	Set Philippines-specific CoMo model simulation vaccination intervention parameters
ph_set_interventions()	Set Philippines-specific CoMo model simulation intervention parameters
ph_set_params()	Interactive guidance for setting Philppines-specific CoMo model parameters
ph_create_params()	Output cases and severity-mortality input tables compatible with CoMo template
Datasets
dataSources	Table of data sources used for parameters
population_psa_2015	The Philippines 2015 Census of Population (POPCEN 2015)
population_wpp_2019	The Philippines population for 2020 from the World Population Prospects 2019
births_wpp_2019	The Philippines births by age group of mother for 2020 from the World Population Prospects 2019
deaths_wpp_2019	The Philippines deaths by age group for 2020 from the World Population Prospects 2019