Combine observed data with a single prediction draw

Internally it sums observed counts from the reporting triangle by reference time and adds them to the predicted counts to form a single draw of the nowcast for the final counts by reference time.

Usage

combine_obs_with_pred(
  predicted_counts,
  reporting_triangle,
  ref_time_aggregator = identity,
  delay_aggregator = function(x) rowSums(x, na.rm = TRUE)
)

Arguments

predicted_counts

Vector of predicted counts at each reference time. Note that if using a reference time or delay aggregator function, this is assumed to have already been aggregated.

reporting_triangle

Matrix of the reporting triangle, with rows representing the time points of reference and columns representing the 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).

ref_time_aggregator

Function that operates along the rows (reference times) of the retrospective point nowcast matrix before it has been aggregated across columns (delays). Default is identity which does not aggregate across reference times.

delay_aggregator

Function that operates along the columns (delays) of the retrospective point nowcast matrix after it has been aggregated across reference times. Default is function(x) rowSums(x, na.rm = TRUE).

Value

A vector of predicted counts at each reference time

Examples

pred_counts <- c(10, 20, 30, 40)
reporting_matrix <- matrix(
  c(
    7, 9, 4, 3,
    1, 2, 3, 4,
    5, 6, 7, 8,
    9, 10, 11, 12
  ),
  nrow = 4,
  byrow = TRUE
)
reporting_triangle <- construct_triangle(reporting_matrix)
combine_obs_with_pred(pred_counts, reporting_triangle)
#> [1] 33 26 41 49
# Another example with rolling sum
if (requireNamespace("zoo", quietly = TRUE)) {
  combine_obs_with_pred(pred_counts,
    reporting_triangle,
    ref_time_aggregator = function(x) zoo::rollsum(x, k = 2, align = "right")
  )
}
#> Warning: longer object length is not a multiple of shorter object length
#> [1] 36 34 44 66