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Tidy a nowcast produced by run_nowcast() or nowcast_ensemble()

tidy.tbl_nowcast.Rd

[Experimental]

Turns a tbl_nowcast into the same table every other tidy() method in this package returns, so a nowcast produced through run_nowcast() and one produced by calling a modelling package by hand are read the same way.

Arguments

x

A tbl_nowcast.

probs

Optional numeric vector of probabilities in [0, 1], adding one q* column each. Only available when the nowcast carries draws: a quantile-only nowcast cannot produce a level it was not summarised at, so asking for one is an error rather than an interpolation dressed up as a quantile.

...

Unused, for generic consistency.

Value

A tibble, as described in Value.

Value

A tibble with the columns documented at tidy.nowcast(): event_date, stratum, estimate, conf.low, conf.high, level and engine, plus one q* column per element of probs.

Two of those columns are read off the object rather than assumed:

level

A tbl_nowcast holds whatever quantile levels it was summarised at, and those need not be symmetric. level is the width of the widest symmetric pair actually present – 0.95 for the default nowcast_quantile_levels(), 0.8 for a fit summarised at c(0.1, 0.5, 0.9). When no symmetric pair exists, level, conf.low and conf.high are all NA: a guessed width defeats the point of the column.

engine

The nowcast's method, so "baselinenowcast" for a single fit and "ensemble" (or whatever name nowcast_ensemble() was given) for a combined one.

stratum is "all" only when the nowcast declares no strata. Several strata columns are pasted " | "-separated, matching the rest of the package, so (stratum, event_date) is a unique key.

estimate is the 0.5 quantile, and NA when the nowcast was summarised at levels that do not include the median.

See also

tidy.nowcast() for the same table off a raw engine fit, run_nowcast(), nowcast_ensemble().

Examples

predictions <- tidyr::expand_grid(
  onset_week = as.Date("2020-01-05") + c(0, 7),
  .quantile_level = c(0.025, 0.5, 0.975)
)
predictions$.value <- c(5, 10, 18, 6, 12, 21)
nc <- tbl_nowcast(
  predictions = predictions, method = "toy", event_date = "onset_week"
)

tidy(nc)
#> # A tibble: 2 × 7
#>   event_date stratum estimate conf.low conf.high level engine
#>   <date>     <chr>      <dbl>    <dbl>     <dbl> <dbl> <chr> 
#> 1 2020-01-05 all           10        5        18  0.95 toy   
#> 2 2020-01-12 all           12        6        21  0.95 toy