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Replace ILINet data with nowcast

Source: R/utils.R
replace_ili_nowcast.Rd

This function replaces the weighted ILI retrieved from get_cdc_ili with nowcast data for each of the locations in the original data. The function will first attempt to use ILI Nearby nowcasts pulled using get_nowcast_ili. If the ILI Nearby nowcasts are unavailable, the function will optionally fallback to a pseudo nowcast method that averages the observed ILI for the 4 most recent weeks. The nowcast data will be used to add 1 additional week to the observed ILI data and (optionally) replace the number of weeks specified in the "weeks_to_replace" argument.

Usage

replace_ili_nowcast(
  ilidat,
  start_date = NULL,
  weeks_to_replace = 1,
  fallback = TRUE,
  try_api = TRUE
)

Arguments

ilidat

ILI data retrieved via get_cdc_ili

start_date

Date from which to start nowcasting; default is lubridate::today

weeks_to_replace

Number of weeks of ilidat to replace; default is 1

fallback

Logical as to whether or not to fall back to pseudo nowcast (average of last 4 ILI weeks in the given location) if nowcast data is unavailable; default is TRUE

try_api

Logical as to whether or not the function should try the ILI Nearby nowcast API; default is TRUE; if FALSE then the function will not attempt to query the API at all

Value

A tibble with the following columns:

  • location: FIPS code for the location

  • region_type: The type of location

  • abbreviation: Abbreviation for the location

  • region: Name of the region

  • 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

  • weighted_ili: Population-weighted percentage of ILI outpatient visits

Examples

if (FALSE) { # \dontrun{
ilidat <- get_cdc_ili(years=2021)
ilidat <-
  ilidat %>%
  dplyr::filter(location=="US" | abbreviation=="VA") %>%
  dplyr::group_by(location) %>%
  dplyr::slice_max(week_start, n=4) %>%
  dplyr::select(location:weighted_ili)
ilidat
iliaug <- replace_ili_nowcast(ilidat, weeks_to_replace=1)
iliaug
} # }