Construct a lookup of references dates by report

Construct a lookup of references dates by report

Usage

enw_reference_by_report(
  missing_reference,
  reps_with_complete_refs,
  metareference,
  max_delay
)

Arguments

missing_reference

missing_reference data.frame output from enw_preprocess_data().

reps_with_complete_refs

A data.frame of report dates with complete (i.e fully reported) reference dates as produced using enw_reps_with_complete_refs().

metareference

metareference data.frame output from enw_preprocess_data().

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).

Value

A wide data.frame with each row being a complete report date and' the columns being the observation index for each reporting delay

See also

Helper functions for model modules add_max_observed_delay(), add_pmfs(), convolution_matrix(), enw_reps_with_complete_refs(), extract_obs_metadata(), extract_sparse_matrix(), latest_obs_as_matrix()