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Calculate reporting delay metadata for a given maximum delay

Source: R/preprocess.R
enw_metadata_delay.Rd

Calculate delay metadata based on the supplied maximum delay and independent of other metadata or date indexing. These data are meant to be used in conjunction with metadata on the date of reference. Users can build additional features with this data.frame or regenerate it using this function in the output of enw_preprocess_data().

Usage

enw_metadata_delay(max_delay = 20, breaks = 4, timestep = "day")

Arguments

max_delay

The maximum delay to model in the delay distribution, specified in units of the timestep (e.g., if timestep = "week", then max_delay = 3 means 3 weeks). If not specified the maximum observed delay is assumed to be the true maximum delay in the model. Otherwise, an integer greater than or equal to 1 can be specified. Observations with delays larger than 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.

Steps to take to determine the maximum delay:

  • Consider what is realistic and relevant for your application.

  • Check the proportion of observations reported (prop_reported) by delay in the new_confirm output of enw_preprocess_obs.

  • Use check_max_delay() to check the coverage of a candidate max_delay.

  • If 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 intervals (i.e. a max_delay of 1 corresponds to no delay).

breaks

Numeric, defaults to 4. The number of breaks to use when constructing a categorised version of numeric delays.

timestep

The timestep to used. This can be a string ("day", "week") or a numeric whole number representing the number of days. Note that "month" is not currently supported in user-facing functions and will throw an error if used.

Value

A data.frame of delay metadata. This includes:

  • delay: The numeric delay from reference date to report.

  • delay_cat: The categorised delay. This may be useful for model building.

  • delay_week: The numeric week since the delay was reported. This again may be useful for model building.

  • delay_head: A logical variable defining if the delay is in the lower 25% of the potential delays. This may be particularly useful when building models that assume a parametric distribution in order to increase the weight of the head of the reporting distribution in a pragmatic way.

  • delay_tail: A logical variable defining if the delay is in the upper 75% of the potential delays. This may be particularly useful when building models that assume a parametric distribution in order to increase the weight of the tail of the reporting distribution in a pragmatic way.

See also

Preprocessing functions enw_add_delay(), enw_add_max_reported(), enw_add_metaobs_features(), 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_missing_reference(), enw_preprocess_data(), enw_reporting_triangle(), enw_reporting_triangle_to_long()

Examples

enw_metadata_delay(max_delay = 20, breaks = 4)
#>     delay delay_cat delay_week delay_head delay_tail
#>     <int>    <fctr>      <int>     <lgcl>     <lgcl>
#>  1:     0     [0,5)          0       TRUE      FALSE
#>  2:     1     [0,5)          0       TRUE      FALSE
#>  3:     2     [0,5)          0       TRUE      FALSE
#>  4:     3     [0,5)          0       TRUE      FALSE
#>  5:     4     [0,5)          0       TRUE      FALSE
#>  6:     5    [5,10)          0      FALSE      FALSE
#>  7:     6    [5,10)          0      FALSE      FALSE
#>  8:     7    [5,10)          1      FALSE      FALSE
#>  9:     8    [5,10)          1      FALSE      FALSE
#> 10:     9    [5,10)          1      FALSE      FALSE
#> 11:    10   [10,15)          1      FALSE      FALSE
#> 12:    11   [10,15)          1      FALSE      FALSE
#> 13:    12   [10,15)          1      FALSE      FALSE
#> 14:    13   [10,15)          1      FALSE      FALSE
#> 15:    14   [10,15)          2      FALSE      FALSE
#> 16:    15   [15,20)          2      FALSE       TRUE
#> 17:    16   [15,20)          2      FALSE       TRUE
#> 18:    17   [15,20)          2      FALSE       TRUE
#> 19:    18   [15,20)          2      FALSE       TRUE
#> 20:    19   [15,20)          2      FALSE       TRUE
#>     delay delay_cat delay_week delay_head delay_tail