get_country_cocirculation_data {imprinting}

Get data on the relative circulation of each influenza A subtype

Description

get_country_cocirculation_data() imports data on the fraction of influenza A cases in a specific country and year that were caused by each influenza A subtype (H1N1, H2N2, or H3N2), or group (group 1 or group 2). Group 1 contains H1N1 and H2N2, and group 2 contains H2N2.

Usage

get_country_cocirculation_data(
  country,
  max_year,
  min_samples = 30,
  output_format = "tibble"
)

Arguments

country

country of interest. Run show_available_countries() for a list of valid inputs.

max_year

last year of interest. Results will be generated from 1918:max_year.

min_samples

if fewer than min_samples (default 30) are reported in the country and year of interest, the function will substitute data from the corresponding WHO region.

output_format

can be 'tibble' (the default) or 'matrix' (used mainly for convenience within other functions)

Details

The data come from three sources:

• Historical assumptions: From 1918-1956, we assume only H1N1 circulated. From 1957-1967, we assume only H2N2 circulated. From 1968-1976, we assume only H3N2 circulated.

• Thompson et al. JAMA, 2003: From 1977-1996 we pull data on the relative dominance of H1N1 and H3N2 from Table 1 of Thompson et al. 2003, which reports surveillance data collected in the United States.

• From 1997-present, we pull in country or region-specific data from WHO Flu Mart on the fraction of specimens collected in routine influenza surveillance that test positive for each subtype. Country-specific data are the default. Regional data, then global data are used if the number of country or region-specific specimens is insufficient. get_template_data() imports the data for 1918-1996. get_country_inputs_1997_to_present() and get_regional_inputs_1997_to_present() import the data for 1997 on.

Value

A matrix with rows showing the calendar year, the fraction of influenza A-positive specimens of each subtype (rows A/H1N1, A/H2N2, and A/H3N2), and of each HA group (rows ⁠group 1⁠, and ⁠group 2⁠). Row A should always be 1, as it shows the sum of subtype-specific fractions. Row B is a placeholder whose values are all NA.

See Also

doi:10.1126/science.aag1322Gostic et al. Science, (2016) for detailed methods.

Examples

get_country_cocirculation_data("United States", "2019")
get_country_cocirculation_data("Laos", "2022", min_samples = 40)