Function reference • SaviR

Data Sets and Transforms

get_combined_table(): A function to retrieve a dataframe (df) with combined Case/Death/Vaccine data by country

get_country_coords(): get_country_coords

get_covid_df(): get_covid_df

get_covid_hist(): Retrieve Current and Archival Reports of Various COVID-19 Data

get_gdeltnews(): get_gdeltnews

get_hospdata(): Get hospitalization data from both OWID and ECDC

get_onetable(): Generate COVID-19 Country Metadata Table

owid_testing_meta get_owid_testing_meta(): Our World in Data (OWID) Testing Metadata

get_preferred_testpos7(): get_preferred_testpos7

get_preferred_tests14(): get_preferred_tests14

get_testing(): Get testing data from Our World in Data (OWID) or FIND

get_testing_long(): get_testing_long

get_vax(): get_vax

get_vax_by_type(): Get data on count of vaccinations by vaccine manufacturer from OWID

get_vax_dates(): Get last non-NA date for key vaccination metrics by country

get_vax_manufacturers(): get_vax_manufacturers

calc_add_risk(): calc_add_risk

calc_vax_carryforward(): Carry-Forward vaccination metrics to latest date

calc_window_incidence(): Compute average incidence over a set day interval

calc_window_pct_change(): Compute Percent-change in Cases Over a Specified Window

onetable: Onetable

country_coords: Country Coordinates

Visualizations

Plots

plot_epicurve(): plot_epicurve

plot_epicurve_dailydouble(): plot_epicurve_dailydouble

plot_epicurve_epidouble(): plot_epicurve_epidouble

plot_epicurve_ind(): plot_epicurve_ind

plot_riskmatrix(): plot_riskmatrix

plot_vaxcoverage(): plot_vaxcoverage

plot_vaxcoverage_pop(): plot_vaxcoverage_pop

plot_vaxcurve(): plot_vaxcurve

Maps

map_burden(): Burden Map

map_template(): map_template

map_trend(): map_trend

map_vaccinations(): map_vaccinations

Tables

table_10mostcases() table_10incidence() table_10percentchange(): SaviR Case Tables for Various CDC Documents

table_10vaccinations(): table_10vaccinations

table_countriesofconcern(): table_countriesofconcern

Misc

datasource_lk: A list of all data sources used in the package to be updated as needed.

manual_iso3_lk: Manual ISO 3166-1 alpha-3 country code entries that don't get parsed in get_onetable()

owid_lk: OWID location renamings

who_lk: WHO Country renamings / rebinnings

who_region_lk: WHO "pretty" english region names

income_aes: Aesthetics for World Bank Country income group

state_aes: Aesthetics for US Department of State regions

who_aes: Aesthetics for WHO regions

cia_wfb_addn_countries: Countries with no current UNWPP data that are manually updated here from CIA World Factbook https://www.cia.gov/the-world-factbook/field/population/country-comparison Currently 2022 estimates are being used

onetable_addn_countries: Additional entries not acknowledged by WHO but required to create onetable