Ensures that all reference and report dates are present for
all groups based on the maximum and minimum dates found in the data.
This function may be of use to users when preprocessing their data. In
general all features that you may consider using as grouping variables
or as covariates need to be included in the by
variable.
Arguments
- obs
A
data.frame
containing at least the following variables:reference date
(index date of interest),report_date
(report date for observations), andconfirm
(cumulative observations by reference and report date).- by
A character vector describing the stratification of observations. This defaults to no grouping. This should be used when modelling multiple time series in order to identify them for downstream modelling
- max_delay
The maximum number of days to model in the delay distribution. Must be an integer greater than or equal to 1. Observations with delays larger then the maximum delay will be dropped. If the specified maximum delay is too short, nowcasts can be biased as important parts of the true delay distribution are cut off. At the same time, computational cost scales non-linearly with this setting, so you want the maximum delay to be as long as necessary, but not much longer. Consider what delays are realistic for your application, and when in doubt, check if increasing the maximum delay noticeably changes the delay distribution or nowcasts as estimated by epinowcast. If it does, your maximum delay may still be too short. Note that delays are zero indexed and so include the reference date and
max_delay - 1
other days (i.e. amax_delay
of 1 corresponds to no delay). You can usecheck_max_delay()
to check the coverage of a delay distribution for different maximum delays.- min_date
The minimum date to include in the data. Defaults to the minimum reference date found in the data.
- max_date
The maximum date to include in the data. Defaults to the maximum report date found in the data.
- timestep
The timestep to used. This can be a string ("day", "week", "month") or a numeric whole number representing the number of days.
- missing_reference
Logical, should entries for cases with missing reference date be completed as well?, Default: TRUE
- completion_beyond_max_report
Logical, should entries be completed beyond the maximum date found in the data? Default: FALSE
- flag_observation
Logical, should observations that have been imputed as missing be flagged as not observed?. Makes use of
enw_flag_observed_observations()
to add a.observed
logical vector which indicates if observations have been imputed. This vector can then be passed to theobservation_indicator
argument ofenw_obs()
to control if these observations are used in the likelihood. Default: FALSE
Value
A data.table
with completed entries for all combinations of
reference dates, groups and possible report dates.
See also
Preprocessing functions
enw_add_delay()
,
enw_add_max_reported()
,
enw_add_metaobs_features()
,
enw_assign_group()
,
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_delay()
,
enw_metadata()
,
enw_missing_reference()
,
enw_preprocess_data()
,
enw_reporting_triangle_to_long()
,
enw_reporting_triangle()
Examples
obs <- data.frame(
report_date = c("2021-10-01", "2021-10-03"), reference_date = "2021-10-01",
confirm = 1
)
enw_complete_dates(obs)
#> Key: <reference_date, report_date>
#> report_date reference_date confirm
#> <IDat> <IDat> <num>
#> 1: 2021-10-01 <NA> 0
#> 2: 2021-10-02 <NA> 0
#> 3: 2021-10-03 <NA> 0
#> 4: 2021-10-01 2021-10-01 1
#> 5: 2021-10-02 2021-10-01 1
#> 6: 2021-10-03 2021-10-01 1
#> 7: 2021-10-02 2021-10-02 0
#> 8: 2021-10-03 2021-10-02 0
#> 9: 2021-10-03 2021-10-03 0
# Allow completion beyond the maximum date found in the data
enw_complete_dates(obs, completion_beyond_max_report = TRUE, max_delay = 10)
#> Key: <reference_date, report_date>
#> report_date reference_date confirm
#> <IDat> <IDat> <num>
#> 1: 2021-10-01 <NA> 0
#> 2: 2021-10-02 <NA> 0
#> 3: 2021-10-03 <NA> 0
#> 4: 2021-10-01 2021-10-01 1
#> 5: 2021-10-02 2021-10-01 1
#> 6: 2021-10-03 2021-10-01 1
#> 7: 2021-10-04 2021-10-01 1
#> 8: 2021-10-05 2021-10-01 1
#> 9: 2021-10-06 2021-10-01 1
#> 10: 2021-10-07 2021-10-01 1
#> 11: 2021-10-08 2021-10-01 1
#> 12: 2021-10-09 2021-10-01 1
#> 13: 2021-10-10 2021-10-01 1
#> 14: 2021-10-11 2021-10-01 1
#> 15: 2021-10-02 2021-10-02 0
#> 16: 2021-10-03 2021-10-02 0
#> 17: 2021-10-04 2021-10-02 0
#> 18: 2021-10-05 2021-10-02 0
#> 19: 2021-10-06 2021-10-02 0
#> 20: 2021-10-07 2021-10-02 0
#> 21: 2021-10-08 2021-10-02 0
#> 22: 2021-10-09 2021-10-02 0
#> 23: 2021-10-10 2021-10-02 0
#> 24: 2021-10-11 2021-10-02 0
#> 25: 2021-10-12 2021-10-02 0
#> 26: 2021-10-03 2021-10-03 0
#> 27: 2021-10-04 2021-10-03 0
#> 28: 2021-10-05 2021-10-03 0
#> 29: 2021-10-06 2021-10-03 0
#> 30: 2021-10-07 2021-10-03 0
#> 31: 2021-10-08 2021-10-03 0
#> 32: 2021-10-09 2021-10-03 0
#> 33: 2021-10-10 2021-10-03 0
#> 34: 2021-10-11 2021-10-03 0
#> 35: 2021-10-12 2021-10-03 0
#> 36: 2021-10-13 2021-10-03 0
#> report_date reference_date confirm