Convert between tbl_now and tsibble

A tsibble::tsibble() has a single time index and a key identifying each series. Nowcasting needs two time indices, so the conversion keeps both date columns: the index is the event date and the report date (plus any strata) becomes part of the key.

tbl_now_from_tsibble() converts a tbl_ts into a tbl_now. You must say which column is the report_date; event_date defaults to the tsibble's index (tsibble::index_var()).

tbl_now_to_tsibble() converts a tbl_now into a tbl_ts, using index ("event_date", the default, or "report_date") as the tsibble index and the other date plus the strata as the key. Linelist data is aggregated to count-incidence first (a tsibble requires unique index/key combinations). The covariates, the censoring indicator and any materialised temporal-effect columns (see compute_temporal_effects()) ride along as measurement columns.

Usage

tbl_now_from_tsibble(
  data,
  report_date,
  event_date = NULL,
  strata = NULL,
  ...,
  verbose = TRUE
)

tbl_now_to_tsibble(
  x,
  ...,
  index = c("event_date", "report_date"),
  verbose = TRUE
)

Arguments

data

A tbl_ts (tsibble).

report_date

The report-date column (required for from), as a tidy-select expression – a bare column name or a string.

event_date

The event-date column (for from), as a tidy-select expression – a bare column name or a string. Defaults to the tsibble index.

strata

Optional character vector of strata columns (from). If NULL (default) the tsibble key columns other than the date columns are used.

...

Forwarded to as_tbl_now() (from) or tsibble::as_tsibble() (to).

verbose

Logical. Print the choices that were made.

x

A tbl_now object.

index

For to: which date becomes the tsibble index, "event_date" (default) or "report_date".

Value

A tbl_now (from) or a tbl_ts (to).

Censored delays

A censoring indicator that is a property of the case rather than of the delay – an administrative "this date is only an upper bound" mark, say – puts a censored and an uncensored row in the same (event_date, report_date) cell. A reporting triangle has one slot per cell, so the extra dimension has to go before the conversion. It is removed automatically, with a warning either way:

• count data: the counts are summed over the flag, leaving case totals unchanged;

• line lists: the column is dropped, leaving one row per case.

tbl_now_to_epidist() is the exception and keeps the flag: estimating a delay distribution is the one job that can use it.

See also

as_tsibble(), the tsibble method that calls this; to_count(), since a tsibble needs unique index/key rows and a line list has to be aggregated first; align_weeks() for regular weekly indexes. as_tbl_now() for the generic that dispatches to the *_from_*() side; run_nowcast(), which does the conversion for you when you fit through an engine(). The One dataset, many nowcasts article fits the same data with every supported package.

Examples

data(denguedat)
nowobj <- tbl_now(denguedat,
  event_date = "onset_week",
  report_date = "report_week", verbose = FALSE
)
# The tsibble is indexed by the event date; the report date is in the key.
ts   <- tbl_now_to_tsibble(nowobj, verbose = FALSE)
#> Warning: tsibble requires unique index/key rows; aggregating linelist to
#> "count-incidence" with `to_count()`.
back <- tbl_now_from_tsibble(ts, report_date = "report_week", verbose = FALSE)