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Retrieve clinical laboratory percent positive flu data

Source: R/retrieve.R
get_cdc_clin.Rd

This function returns weekly state and/or national clinical laboratory percent positivity data from the NREVSS reporting instrument via the CDC FluView API.

Usage

get_cdc_clin(region = "both", years = NULL)

Arguments

region

Either "state", "national", or "both". Defaults to "both" to return state and national data combined.

years

A vector of years to retrieve data for. CDC has data going back to 1997. Default value (NULL) retrieves all years.

Value

A tibble with the following columns:

  • abbreviation: Abbreviation for the location

  • location: FIPS code for the location

  • epiyear: Year of reporting (in epidemiological week calendar)

  • epiweek: Week of reporting (in epidemiological week calendar)

  • week_start: Date of beginning (Sunday) of the given epidemiological week

  • p_positive: Percentage of positive specimens

  • n_positive: Total number of positive specimens

  • total: Total number of specimens tested

References

https://gis.cdc.gov/grasp/fluview/Phase_6_Cleared_Help.pdf

Examples

if (FALSE) { # \dontrun{
# Get all clinical lab flu positivity data
all_clin <- get_cdc_clin()
all_clin
# Alternatively look at a specific location and time
# This 2021 will return weekly data
# Starting at beginning of 2021/22 season
# Ending the week before start of 2022/23 season
va_clin <-
  get_cdc_clin(region = "state", years = 2021) %>%
  dplyr::filter(location == "51")
va_clin
} # }