baselinenowcast (version 0.2.0)

estimate_and_apply_uncertainty: Estimate and apply uncertainty to a point nowcast matrix

Description

Generates probabilistic nowcasts by estimating uncertainty parameters from retrospective nowcasts and applying them to a point nowcast matrix.

This function combines:

1. estimate_uncertainty_retro() - Estimates uncertainty parameters using retrospective nowcasts

2. sample_nowcasts() - Applies uncertainty to generate draws

To obtain estimates of uncertainty parameters, use estimate_uncertainty_retro(). For full control over individual steps (e.g., custom matrix preparation, alternative aggregation), use the low-level functions (truncate_to_rows(), apply_reporting_structures(), estimate_and_apply_delays(), estimate_uncertainty()) directly.

Usage

estimate_and_apply_uncertainty(
  point_nowcast_matrix,
  reporting_triangle,
  n_history_delay,
  n_retrospective_nowcasts,
  structure = get_reporting_structure(reporting_triangle),
  draws = 1000,
  delay_pmf = NULL,
  uncertainty_model = fit_by_horizon,
  uncertainty_sampler = sample_nb,
  validate = TRUE,
  ...
)

Value

nowcast_draws_df Dataframe containing draws of combined observations and probabilistic predictions at each reference time.

Arguments

point_nowcast_matrix

Matrix of point nowcast predictions and observations, with rows representing the reference times and columns representing the delays.

reporting_triangle

A reporting_triangle object with rows representing reference times and columns representing delays. Can be a reporting matrix or incomplete reporting matrix. Can also be a ragged reporting triangle, where multiple columns are reported for the same row (e.g., weekly reporting of daily data).

n_history_delay

Integer indicating the number of reference times (observations) to be used in the estimate of the reporting delay, always starting from the most recent reporting delay.

n_retrospective_nowcasts

Integer indicating the number of retrospective nowcast times to use for uncertainty estimation.

structure

Integer or vector specifying the reporting structure. If integer, divides columns evenly by that integer (with last possibly truncated). If vector, the sum must not be greater than or equal to the number of columns. Default is 1 (standard triangular structure).

draws

Integer indicating the number of draws of the predicted nowcast vector to generate. Default is 1000.

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.

uncertainty_model

Function that ingests a matrix of observations and a matrix of predictions and returns a vector that can be used to apply uncertainty using the same error model. Default is fit_by_horizon with arguments of obs matrix of observations and pred the matrix of predictions that fits each column (horizon) to a negative binomial observation model by default. The user can specify a different fitting model by replacing the fit_model argument in fit_by_horizon.

uncertainty_sampler

Function that ingests a vector or matrix of predictions and a vector of uncertainty parameters and generates draws from the observation model. Default is sample_nb which expects arguments pred for the vector of predictions and uncertainty parameters for the corresponding vector of uncertainty parameters, and draws from a negative binomial for each element of the vector.

validate

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

...

Additional arguments to estimate_uncertainty() and sample_prediction().

See Also

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

Examples

# Use package data truncated to appropriate size
data_as_of <- syn_nssp_df[syn_nssp_df$report_date <= "2026-04-01", ]
triangle <- as_reporting_triangle(data_as_of) |>
  truncate_to_delay(max_delay = 25)

pt_nowcast_matrix <- estimate_and_apply_delay(
  reporting_triangle = triangle,
  n = 75
)
# Use 75 reference times for delay estimation and 40 for uncertainty
nowcast_draws_df <- estimate_and_apply_uncertainty(
  pt_nowcast_matrix,
  triangle,
  n_history_delay = 75,
  n_retrospective_nowcasts = 40,
  draws = 100
)
head(nowcast_draws_df)