Convert between tbl_now and baselinenowcast — tbl_now

tbl_now_from_baselinenowcast() accepts either the long data.frame (reference_date, report_date, count) or a reporting_triangle matrix (rownames = reference dates, colnames = delays, incremental counts) and converts it into a tbl_now of data_type = "count-incidence".

tbl_now_to_baselinenowcast() returns either a reporting_triangle matrix (format = "matrix", the default) via baselinenowcast::as_reporting_triangle(), or the long baselinenowcast-style data.frame (format = "long"). The long format also carries the covariates, the censoring indicator and any materialised temporal-effect columns (see compute_temporal_effects()); the matrix holds only the three core columns.

Usage

tbl_now_from_baselinenowcast(
  data,
  ...,
  reference_date = "reference_date",
  report_date = "report_date",
  count = "count",
  delays_unit = "days",
  verbose = TRUE
)

tbl_now_to_baselinenowcast(
  x,
  ...,
  format = c("matrix", "long"),
  delays_unit = "days",
  verbose = TRUE
)

Arguments

data: A long data.frame or a reporting_triangle matrix.
...: Forwarded to as_tbl_now() (from) or baselinenowcast::as_reporting_triangle() (to, matrix format).
reference_date, report_date, count: Column names (long format only).
delays_unit: Unit of the delay axis (passed to baselinenowcast::as_reporting_triangle()). Defaults to "days".
verbose: Logical. Print the choices that were made.
x: A tbl_now object.
format: For to: "matrix" (default) or "long".

Value

A tbl_now (from), or a data.frame/reporting_triangle (to).

Round-trip

A reporting_triangle distinguishes not-yet-observed cells (NA) from observed zeros (0). The NA cells split at the last observed report date (the latest report with a non-NA count, taken as the nowcast's now):

cells with report_date > now are * not-yet-observable* future cells. They are dropped from the tbl_now().
cells with report_date <= now could have been reported but were not. They are genuinely missing and kept as count = NA rows in the tbl_now().

On the way back, baselinenowcast::as_reporting_triangle() fills the in-triangle cells with 0 unless they are marked in the tibble as NA.

Examples

# Get a reporting triangle example
rt     <- baselinenowcast::example_reporting_triangle

# Convert to a tbl_now
nowobj <- tbl_now_from_baselinenowcast(rt)
#> 
#> ── Converted baselinenowcast <data> into a <tbl_now> 
#> • event_date: "reference_date"
#> • report_date: "report_date"
#> • data_type: "count-incidence"
#> • now: "2024-01-07"
#> • event_units: "days"
#> • report_units: "days"
#> • case_count: "count"
#> • expanded a reporting-triangle matrix to long counts

# The matrix round-trip is faithful (not-yet-observed `NA` cells are kept).
identical(rt, tbl_now_to_baselinenowcast(nowobj))
#> 
#> ── Converting <tbl_now> to baselinenowcast matrix 
#> • reference_date <- "reference_date"
#> • report_date <- "report_date"
#> • count <- "count"
#> • format: "matrix"
#> ℹ Using max_delay = 3 from data
#> [1] TRUE