This function provides a naive nowcasting method for clinical laboratory percent positive flu data. The methodology simply averages the last 4 weeks of available data and uses this average as the value for the number of weeks specified to replace. The function will always add 1 additional week to the observed data and (optionally) replace the number of weeks specified in the "weeks_to_replace" argument. This is useful given that there is reporting lag in the NREVSS clinical laboratory percent positive flu data.
Arguments
- clin
Data prepared with get_cdc_clin
- weeks_to_replace
Number of retrospective weeks to replace with nowcast; default is
1
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
Examples
if (FALSE) { # \dontrun{
# Get data for Texas
tx_clin <-
get_cdc_clin(region = "state") %>%
dplyr::filter(location == "48")
# Look at most recent observations
tx_clin %>%
dplyr::arrange(week_start) %>%
tail()
# Now augment with default 1 week nowcast
tx_clin %>%
clin_nowcast(., weeks_to_replace = 1) %>%
dplyr::arrange(week_start) %>%
tail()
# And again augmented with 2 week nowcast instead
tx_clin %>%
clin_nowcast(., weeks_to_replace = 2) %>%
dplyr::arrange(week_start) %>%
tail()
} # }