One surveillance line list per stratum

The object returned by tbl_now_to_surveillance(x, format = "linelist_list"): one individual-level line list per observed combination of the object's strata, together with the metadata needed to rebuild a tbl_now from it.

It is a thin class – it is still a list of plain data frames, so lapply(), [[ and friends work as usual:

pieces <- tbl_now_to_surveillance(x, format = "linelist_list")
lapply(pieces, function(piece) {
  surveillance::nowcast(
    now = get_now(x), when = get_surveillance_when(x),
    data = piece, dEventCol = "dHospital", dReportCol = "dReport",
    control = list(dRange = get_surveillance_range(x))
  )
})

The class exists for the same reason tbl_now_triangle_list does: printing says plainly that these are strata rather than something else shaped like a list of line lists, and it carries the now, the units and the original date-column names, none of which survive in a bare split().

now and the time grid are deliberately not baked into each piece. The grid must come from the whole object (get_surveillance_range()), not from the piece: every stratum has to be laid on the same axis, or a stratum whose first case arrived late starts its own time on a different day.

as_tbl_now() binds the pieces back together and restores the original date-column names, the strata and the covariates. Two things do not survive, because they are not in the line list to survive: count input comes back as a "linelist" (one row per case, so the totals are unchanged but the case_count column is gone), and materialised temporal-effect columns come back as ordinary columns rather than as a spec.

Usage

# S3 method for class 'tbl_now_surveillance_list'
print(x, ...)

Arguments

x: A tbl_now_surveillance_list.
...: Ignored.

Value

print() returns x invisibly.

Examples

data(denguedat)
dengue <- tbl_now(denguedat[1:3000, ],
  event_date = onset_week, report_date = report_week, verbose = FALSE
)

## One line list per stratum, in the shape surveillance::nowcast() wants.
linelists <- tbl_now_to_surveillance(dengue,
  format = "linelist_list", verbose = FALSE
)

# Printing summarises the set rather than dumping every data frame.
linelists
#> ── 1 surveillance line list from a <tbl_now> ───────────────────────────────────
#> • No strata; a single line list named "all"
#> • Date columns: "dHospital" (event), "dReport" (report)
#> • Rows each: 3000
#> • Now: "1991-10-14"
#> ℹ `lapply()` over this, passing `control$dRange = get_surveillance_range(x)` from the WHOLE object so every stratum shares one time axis.

length(linelists)
#> [1] 1
head(linelists[[1]])
#>    dHospital    dReport
#> 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

Usage

Arguments

Value

See also

Examples