enw_add_metaobs_features: Add common metadata variables

In seabbs/epinowcast: Flexible Hierarchical Nowcasting

Add common metadata variables

Description

If not already present, annotates time series data with metadata commonly used in models: day of week, and days, weeks, and months since start of time series.

Usage

enw_add_metaobs_features(
  metaobs,
  holidays = NULL,
  holidays_to = "Sunday",
  datecol = "date"
)

Arguments

metaobs	Raw data, coercible via data.table::as.data.table(). Coerced object must have Dates column corresponding to datecol name.
holidays	a (potentially empty) vector of dates (or input coercible to such; see coerce_date()). The day_of_week column will be set to holidays_to for these dates.
holidays_to	A character string to assign to holidays, when holidays argument non-empty. Replaces the day_of_week column value
datecol	The column in metaobs corresponding to pertinent dates.

Details

Effects models often need to include covariates for time-based features, such as day of the week (e.g. to reflect different care-seeking and/or reporting behaviour).

This function is called from within enw_preprocess_data() to systematically annotate metaobs with these commonly used metadata, if not already present.

However, it can also be used directly on other data.

Value

A copy of the metaobs input, with additional columns:

• day_of_week, a factor of values as output from weekdays() and possibly as holiday_to if distinct from weekdays values

• day, numeric, 0 based from start of time series

• week, numeric, 0 based from start of time series

• month, numeric, 0 based from start of time series

See Also

Preprocessing functions enw_add_delay(), enw_add_max_reported(), enw_assign_group(), enw_complete_dates(), enw_construct_data(), enw_extend_date(), enw_filter_delay(), enw_filter_reference_dates(), enw_filter_report_dates(), enw_flag_observed_observations(), enw_impute_na_observations(), enw_latest_data(), enw_metadata(), enw_metadata_delay(), enw_missing_reference(), enw_preprocess_data(), enw_reporting_triangle(), enw_reporting_triangle_to_long()

Examples

# make some example date
nat_germany_hosp <- subset(
  germany_covid19_hosp,
  location == "DE" & age_group == "80+"
)[1:40]

basemeta <- enw_add_metaobs_features(
  nat_germany_hosp,
  datecol = "report_date"
)
basemeta

# with holidays - n.b.: holidays not found are silently ignored
holidaymeta <- enw_add_metaobs_features(
  nat_germany_hosp,
  datecol = "report_date",
  holidays = c(
    "2021-04-04", "2021-04-05",
    "2021-05-01", "2021-05-13",
    "2021-05-24"
  ),
  holidays_to = "Holiday"
)
holidaymeta
subset(holidaymeta, day_of_week == "Holiday")

seabbs/epinowcast documentation built on Feb. 3, 2025, 9:56 p.m.