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 = c(),
holidays_to = "Sunday",
datecol = "date"
)Arguments
- metaobs
Raw data, coercible via
data.table::as.data.table(). Coerced object must have Dates column corresponding todatecolname.- holidays
a (potentially empty) vector of dates (or input coercible to such; see
coerce_date()). Theday_of_weekcolumn will be set toholidays_tofor these dates.- holidays_to
A character string to assign to holidays, when
holidaysargument non-empty. Replaces theday_of_weekcolumn value- datecol
The column in
metaobscorresponding to pertinent dates.
Value
A copy of the metaobs input, with additional columns:
day_of_week, a factor of values as output fromweekdays()and possibly asholiday_toif distinct from weekdays valuesday, numeric, 0 based from start of time seriesweek, numeric, 0 based from start of time seriesmonth, numeric, 0 based from start of time series
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.
See also
Preprocessing functions
enw_add_delay(),
enw_add_max_reported(),
enw_assign_group(),
enw_complete_dates(),
enw_construct_data(),
enw_cumulative_to_incidence(),
enw_delay_filter(),
enw_delay_metadata(),
enw_extend_date(),
enw_filter_reference_dates(),
enw_filter_report_dates(),
enw_incidence_to_cumulative(),
enw_latest_data(),
enw_metadata(),
enw_missing_reference(),
enw_preprocess_data(),
enw_reporting_triangle_to_long(),
enw_reporting_triangle()
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
#> reference_date location age_group confirm report_date day_of_week day week
#> 1: 2021-04-06 DE 80+ 35 2021-04-06 Tuesday 0 0
#> 2: 2021-04-07 DE 80+ 81 2021-04-07 Wednesday 1 0
#> 3: 2021-04-08 DE 80+ 85 2021-04-08 Thursday 2 0
#> 4: 2021-04-09 DE 80+ 62 2021-04-09 Friday 3 0
#> 5: 2021-04-10 DE 80+ 45 2021-04-10 Saturday 4 0
#> 6: 2021-04-11 DE 80+ 23 2021-04-11 Sunday 5 0
#> 7: 2021-04-12 DE 80+ 33 2021-04-12 Monday 6 0
#> 8: 2021-04-13 DE 80+ 66 2021-04-13 Tuesday 7 1
#> 9: 2021-04-14 DE 80+ 50 2021-04-14 Wednesday 8 1
#> 10: 2021-04-15 DE 80+ 66 2021-04-15 Thursday 9 1
#> 11: 2021-04-16 DE 80+ 67 2021-04-16 Friday 10 1
#> 12: 2021-04-17 DE 80+ 50 2021-04-17 Saturday 11 1
#> 13: 2021-04-18 DE 80+ 33 2021-04-18 Sunday 12 1
#> 14: 2021-04-19 DE 80+ 25 2021-04-19 Monday 13 1
#> 15: 2021-04-20 DE 80+ 53 2021-04-20 Tuesday 14 2
#> 16: 2021-04-21 DE 80+ 68 2021-04-21 Wednesday 15 2
#> 17: 2021-04-22 DE 80+ 56 2021-04-22 Thursday 16 2
#> 18: 2021-04-23 DE 80+ 61 2021-04-23 Friday 17 2
#> 19: 2021-04-24 DE 80+ 45 2021-04-24 Saturday 18 2
#> 20: 2021-04-25 DE 80+ 35 2021-04-25 Sunday 19 2
#> 21: 2021-04-26 DE 80+ 17 2021-04-26 Monday 20 2
#> 22: 2021-04-27 DE 80+ 50 2021-04-27 Tuesday 21 3
#> 23: 2021-04-28 DE 80+ 56 2021-04-28 Wednesday 22 3
#> 24: 2021-04-29 DE 80+ 44 2021-04-29 Thursday 23 3
#> 25: 2021-04-30 DE 80+ 54 2021-04-30 Friday 24 3
#> 26: 2021-05-01 DE 80+ 48 2021-05-01 Saturday 25 3
#> 27: 2021-05-02 DE 80+ 27 2021-05-02 Sunday 26 3
#> 28: 2021-05-03 DE 80+ 26 2021-05-03 Monday 27 3
#> 29: 2021-05-04 DE 80+ 55 2021-05-04 Tuesday 28 4
#> 30: 2021-05-05 DE 80+ 59 2021-05-05 Wednesday 29 4
#> 31: 2021-05-06 DE 80+ 58 2021-05-06 Thursday 30 4
#> 32: 2021-05-07 DE 80+ 48 2021-05-07 Friday 31 4
#> 33: 2021-05-08 DE 80+ 34 2021-05-08 Saturday 32 4
#> 34: 2021-05-09 DE 80+ 10 2021-05-09 Sunday 33 4
#> 35: 2021-05-10 DE 80+ 24 2021-05-10 Monday 34 4
#> 36: 2021-05-11 DE 80+ 49 2021-05-11 Tuesday 35 5
#> 37: 2021-05-12 DE 80+ 42 2021-05-12 Wednesday 36 5
#> 38: 2021-05-13 DE 80+ 39 2021-05-13 Thursday 37 5
#> 39: 2021-05-14 DE 80+ 15 2021-05-14 Friday 38 5
#> 40: 2021-05-15 DE 80+ 23 2021-05-15 Saturday 39 5
#> reference_date location age_group confirm report_date day_of_week day week
#> month
#> 1: 0
#> 2: 0
#> 3: 0
#> 4: 0
#> 5: 0
#> 6: 0
#> 7: 0
#> 8: 0
#> 9: 0
#> 10: 0
#> 11: 0
#> 12: 0
#> 13: 0
#> 14: 0
#> 15: 0
#> 16: 0
#> 17: 0
#> 18: 0
#> 19: 0
#> 20: 0
#> 21: 0
#> 22: 0
#> 23: 0
#> 24: 0
#> 25: 0
#> 26: 1
#> 27: 1
#> 28: 1
#> 29: 1
#> 30: 1
#> 31: 1
#> 32: 1
#> 33: 1
#> 34: 1
#> 35: 1
#> 36: 1
#> 37: 1
#> 38: 1
#> 39: 1
#> 40: 1
#> month
# 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
#> reference_date location age_group confirm report_date day_of_week day week
#> 1: 2021-04-06 DE 80+ 35 2021-04-06 Tuesday 0 0
#> 2: 2021-04-07 DE 80+ 81 2021-04-07 Wednesday 1 0
#> 3: 2021-04-08 DE 80+ 85 2021-04-08 Thursday 2 0
#> 4: 2021-04-09 DE 80+ 62 2021-04-09 Friday 3 0
#> 5: 2021-04-10 DE 80+ 45 2021-04-10 Saturday 4 0
#> 6: 2021-04-11 DE 80+ 23 2021-04-11 Sunday 5 0
#> 7: 2021-04-12 DE 80+ 33 2021-04-12 Monday 6 0
#> 8: 2021-04-13 DE 80+ 66 2021-04-13 Tuesday 7 1
#> 9: 2021-04-14 DE 80+ 50 2021-04-14 Wednesday 8 1
#> 10: 2021-04-15 DE 80+ 66 2021-04-15 Thursday 9 1
#> 11: 2021-04-16 DE 80+ 67 2021-04-16 Friday 10 1
#> 12: 2021-04-17 DE 80+ 50 2021-04-17 Saturday 11 1
#> 13: 2021-04-18 DE 80+ 33 2021-04-18 Sunday 12 1
#> 14: 2021-04-19 DE 80+ 25 2021-04-19 Monday 13 1
#> 15: 2021-04-20 DE 80+ 53 2021-04-20 Tuesday 14 2
#> 16: 2021-04-21 DE 80+ 68 2021-04-21 Wednesday 15 2
#> 17: 2021-04-22 DE 80+ 56 2021-04-22 Thursday 16 2
#> 18: 2021-04-23 DE 80+ 61 2021-04-23 Friday 17 2
#> 19: 2021-04-24 DE 80+ 45 2021-04-24 Saturday 18 2
#> 20: 2021-04-25 DE 80+ 35 2021-04-25 Sunday 19 2
#> 21: 2021-04-26 DE 80+ 17 2021-04-26 Monday 20 2
#> 22: 2021-04-27 DE 80+ 50 2021-04-27 Tuesday 21 3
#> 23: 2021-04-28 DE 80+ 56 2021-04-28 Wednesday 22 3
#> 24: 2021-04-29 DE 80+ 44 2021-04-29 Thursday 23 3
#> 25: 2021-04-30 DE 80+ 54 2021-04-30 Friday 24 3
#> 26: 2021-05-01 DE 80+ 48 2021-05-01 Holiday 25 3
#> 27: 2021-05-02 DE 80+ 27 2021-05-02 Sunday 26 3
#> 28: 2021-05-03 DE 80+ 26 2021-05-03 Monday 27 3
#> 29: 2021-05-04 DE 80+ 55 2021-05-04 Tuesday 28 4
#> 30: 2021-05-05 DE 80+ 59 2021-05-05 Wednesday 29 4
#> 31: 2021-05-06 DE 80+ 58 2021-05-06 Thursday 30 4
#> 32: 2021-05-07 DE 80+ 48 2021-05-07 Friday 31 4
#> 33: 2021-05-08 DE 80+ 34 2021-05-08 Saturday 32 4
#> 34: 2021-05-09 DE 80+ 10 2021-05-09 Sunday 33 4
#> 35: 2021-05-10 DE 80+ 24 2021-05-10 Monday 34 4
#> 36: 2021-05-11 DE 80+ 49 2021-05-11 Tuesday 35 5
#> 37: 2021-05-12 DE 80+ 42 2021-05-12 Wednesday 36 5
#> 38: 2021-05-13 DE 80+ 39 2021-05-13 Holiday 37 5
#> 39: 2021-05-14 DE 80+ 15 2021-05-14 Friday 38 5
#> 40: 2021-05-15 DE 80+ 23 2021-05-15 Saturday 39 5
#> reference_date location age_group confirm report_date day_of_week day week
#> month
#> 1: 0
#> 2: 0
#> 3: 0
#> 4: 0
#> 5: 0
#> 6: 0
#> 7: 0
#> 8: 0
#> 9: 0
#> 10: 0
#> 11: 0
#> 12: 0
#> 13: 0
#> 14: 0
#> 15: 0
#> 16: 0
#> 17: 0
#> 18: 0
#> 19: 0
#> 20: 0
#> 21: 0
#> 22: 0
#> 23: 0
#> 24: 0
#> 25: 0
#> 26: 1
#> 27: 1
#> 28: 1
#> 29: 1
#> 30: 1
#> 31: 1
#> 32: 1
#> 33: 1
#> 34: 1
#> 35: 1
#> 36: 1
#> 37: 1
#> 38: 1
#> 39: 1
#> 40: 1
#> month
subset(holidaymeta, day_of_week == "Holiday")
#> reference_date location age_group confirm report_date day_of_week day week
#> 1: 2021-05-01 DE 80+ 48 2021-05-01 Holiday 25 3
#> 2: 2021-05-13 DE 80+ 39 2021-05-13 Holiday 37 5
#> month
#> 1: 1
#> 2: 1