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Format time series forecast

Source: R/submit.R
ts_format_for_submission.Rd

This function specifically formats time series forecasts generated with ts_fit_forecast to adhere to probabilistic forecast submission guidelines for consortia such as FluSight. It is used as a helper in format_for_submission.

Usage

ts_format_for_submission(
  tsfor,
  .target = "wk ahead inc flu hosp",
  .counts = TRUE
)

Arguments

tsfor

The forecast from ts_fit_forecast

.target

Name of the target in the forecast; default is "wk ahead inc flu hosp"

.counts

Logical; default TRUE indicates that the target outcome is a count, and should be rounded off at an integer

Value

A named list of tibbles with probabilistic forecasts (one for each model), formatted for submission with the following columns:

  • forecast_date: Date of forecast

  • target: Horizon and name of forecasted target

  • target_end_date: Last date of the forecasted target (e.g., Saturday of the given epidemiological week)

  • location: FIPS code for location

  • type: One of either "point" or "quantile" for the forecasted value

  • quantile: The quantile for the forecasted value; NA if "type" is "point"

  • value: The forecasted value

Details

Uses quantiles c(0.01, 0.025, seq(0.05, 0.95, by = 0.05), 0.975, 0.99) in the built-in fiphde:::q, using an accessory table fiphde:::quidk.

References

https://github.com/cdcepi/Flusight-forecast-data/blob/master/data-forecasts/README.md

Examples

if (FALSE) { # \dontrun{
# Get raw data from healthdata.gov
h_raw <- get_hdgov_hosp(limitcols=TRUE)

# Prep, and make a tsibble
prepped_hosp <- prep_hdgov_hosp(h_raw, statesonly=TRUE)
prepped_hosp_tsibble <- make_tsibble(prepped_hosp,
                                     epiyear = epiyear,
                                     epiweek=epiweek,
                                     key=location)
# Limit to only Virginia and US
prepped_hosp_tsibble <-
  prepped_hosp_tsibble %>%
  dplyr::filter(location %in% c("US", "51"))

# Fit a model
hosp_fitfor <- ts_fit_forecast(prepped_hosp_tsibble,
                               horizon=4L,
                               outcome="flu.admits",
                               covariates=TRUE)

# Format for submission
formatted_list <- ts_format_for_submission(hosp_fitfor$tsfor)
formatted_list
} # }