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.
get_country_cocirculation_data(
country,
max_year,
min_samples = 30,
output_format = "tibble"
)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.
country of interest. Run show_available_countries() for a list of valid inputs.
last year of interest. Results will be generated from 1918:max_year.
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.
can be 'tibble' (the default) or 'matrix' (used mainly for convenience within other functions)
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.
tools:::Rd_expr_doi("https://doi.org/10.1126/science.aag1322")Gostic et al. Science, (2016) for detailed methods.
get_country_cocirculation_data("United States", "2019")
get_country_cocirculation_data("Laos", "2022", min_samples = 40)
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