baselinenowcast (version 0.2.0)

estimate_and_apply_delays: Estimate and apply delays to generate retrospective nowcasts

Description

This function ingests a list of incomplete reporting triangles and generates a list of point nowcast matrices, based on the delay estimated in each triangle or the corresponding delay passed in. It uses the specified n number of reference times to estimate the delay in each retrospective reporting triangle.

Usage

estimate_and_apply_delays(
  retro_reporting_triangles,
  n = min(sapply(retro_reporting_triangles, nrow)),
  delay_pmf = NULL,
  validate = TRUE
)

Value

point_nowcast_matrices List of the same number of elements as the input retro_reporting_triangles but with each reporting triangle filled in based on the delay estimated in that reporting triangle.

Arguments

retro_reporting_triangles

List of reporting triangles to generate nowcasts for. Typically created by apply_reporting_structures().

n

Integer indicating the number of reference times (number of rows) to use to estimate the delay distribution for each reporting triangle. Default is the minimum of the number of rows of all the matrices in retro_reporting_triangles.

delay_pmf

Vector or list of vectors of delays assumed to be indexed starting at the first delay column in each of the matrices in retro_reporting_triangles. If a list, must be of the same length as retro_reporting_triangles, with elements aligning. Default is NULL.

validate

Logical. If TRUE (default), validates the object. Set to FALSE only when called from functions that already validated.

See Also

High-level workflow wrapper functions allocate_reference_times(), estimate_and_apply_delay(), estimate_and_apply_uncertainty(), estimate_uncertainty_retro()

Examples

# Generate retrospective nowcasts using larger triangle
data_as_of <- syn_nssp_df[syn_nssp_df$report_date <= "2026-04-01", ]
rep_tri <- as_reporting_triangle(data_as_of) |>
  truncate_to_delay(max_delay = 25) |>
  tail(n = 50)
trunc_rts <- truncate_to_rows(rep_tri, n = 2)
retro_rts <- apply_reporting_structures(trunc_rts)
retro_pt_nowcast_mat_list <- estimate_and_apply_delays(retro_rts, n = 30)
retro_pt_nowcast_mat_list[1:2]

# Using a pre-computed delay PMF
delay <- estimate_delay(rep_tri, n = 30)
retro_pt_nowcast_mat_list <- estimate_and_apply_delays(
  retro_rts,
  n = 30,
  delay_pmf = delay
)
retro_pt_nowcast_mat_list[1:2]