Convert a tbl_now into the line list NobBS nowcasts from

NobBS::NobBS() counts rows: it takes an individual-level line list with one column for the event date and one for the report date, and treats each row as a case. Handing it count-incidence data directly is therefore silently wrong – a table of 1,174 rows carrying 50,160 cases is nowcast as 1,174 cases. This converter expands counts to one row per case first, so the totals NobBS sees are the totals in your data.

Trim before converting when the series is long: the expansion is one row per case, and NobBS()'s own moving_window only limits what it fits, not what it is handed.

Usage

tbl_now_to_nobbs(
  x,
  ...,
  event_col = "onset_date",
  report_col = "report_date",
  strata_col = "strata",
  strata_sep = " | ",
  verbose = TRUE
)

Arguments

x: A tbl_now.
...: Unused, for extensibility.
event_col, report_col: Names the two date columns should take in the result. The defaults match the arguments of NobBS::NobBS().
strata_col: Name of the single stratifying column to add, holding every declared stratum pasted together. This is what NobBS::NobBS.strat()'s own strata argument takes. NULL leaves it out. Ignored when the object declares no strata.
strata_sep: Separator used to paste the strata into strata_col.
verbose: Print what the conversion did. The units line prints the string NobBS::NobBS() itself accepts ("1 day" or "1 week"), not the object's own "days" / "weeks", so it can be pasted straight into the call.

Value

A data.frame with one row per case, ready for NobBS::NobBS(). The strata, covariates and temporal-effect columns ride along, plus the single pasted strata_col that NobBS::NobBS.strat() takes.

Stratified nowcasts

NobBS::NobBS.strat() fits one nowcast per stratum, and its strata argument names one column. A tbl_now may declare several – age group and region, say – and "nowcast each age-group-and-region separately" is a single stratum as far as NobBS is concerned. So the declared columns are also pasted into one strata column, which you hand straight to NobBS.strat():

nb <- tbl_now_to_nobbs(x, verbose = FALSE)
NobBS::NobBS.strat(nb, now = get_now(x), units = "1 day",
                   onset_date = "onset_date", report_date = "report_date",
                   strata = "strata")

The original columns are kept alongside it, so a hand-rolled per-stratum loop can still split on them. Choose a separator your stratum values do not contain: run_nowcast() splits the label back into the original columns when it tidies the fit.

Units NobBS can model

NobBS::NobBS() documents units as "1 day" or "1 week" and nothing else, so this converter aborts on any other grid rather than hand back a line list NobBS cannot use. That includes a "numeric" grid: its date columns are integer indices, and coercing them with as.Date() would anchor them at the 1970 epoch and return a plausible-looking line list of invented dates. Aggregate to days or weeks first (see align_weeks()).

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.

Examples

data(denguedat)
nowobj <- tbl_now(denguedat,
  event_date = "onset_week", report_date = "report_week", verbose = FALSE
)
nb <- tbl_now_to_nobbs(nowobj, verbose = FALSE)
head(nb)
#>   onset_date report_date
#> 1 1990-01-01  1990-01-01
#> 2 1990-01-01  1990-01-01
#> 3 1990-01-01  1990-01-01
#> 4 1990-01-01  1990-01-08
#> 5 1990-01-01  1990-01-08
#> 6 1990-01-01  1990-01-15

Convert a `tbl_now` into the line list NobBS nowcasts from