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Extract posterior samples for the nowcast prediction

Source: R/postprocess.R
enw_nowcast_samples.Rd

A generic wrapper around posterior::draws_df() with opinionated defaults to extract the posterior samples for the nowcast ("pp_inf_obs" from the stan code). The functionality of this function can be used directly on the output of epinowcast() using the supplied summary.epinowcast() method.

Usage

enw_nowcast_samples(fit, obs, max_delay = NULL, timestep = "day")

Arguments

fit

A cmdstanr fit object.

obs

An observation data.frame containing reference_date columns of the same length as the number of rows in the posterior and the most up to date observation for each date. This is used to align the posterior with the observations. The easiest source of this data is the output of latest output of enw_preprocess_data() or enw_latest_data().

max_delay

Maximum delay to which nowcasts should be summarised. Must be equal (default) or larger than the modelled maximum delay. If it is larger, then nowcasts for unmodelled dates are added by assuming that case counts beyond the modelled maximum delay are fully observed.

timestep

The timestep to used. This can be a string ("day", "week", "month") or a numeric whole number representing the number of days.

Value

A data.frame of posterior samples for the nowcast prediction. This uses observed data where available and the posterior prediction where not.

See also

Functions used for postprocessing of model fits build_ord_obs(), enw_add_latest_obs_to_nowcast(), enw_nowcast_summary(), enw_posterior(), enw_pp_summary(), enw_quantiles_to_long(), enw_summarise_samples(), subset_obs()

Examples

fit <- enw_example("nowcast")
enw_nowcast_samples(
  fit$fit[[1]],
  fit$latest[[1]],
  fit$max_delay,
  "day"
  )
#>        reference_date report_date .group max_confirm location age_group confirm
#>                <IDat>      <IDat>  <num>       <int>   <fctr>    <fctr>   <int>
#>     1:     2021-08-03  2021-08-22      1         149       DE       00+     149
#>     2:     2021-08-03  2021-08-22      1         149       DE       00+     149
#>     3:     2021-08-03  2021-08-22      1         149       DE       00+     149
#>     4:     2021-08-03  2021-08-22      1         149       DE       00+     149
#>     5:     2021-08-03  2021-08-22      1         149       DE       00+     149
#>    ---                                                                         
#> 19996:     2021-08-22  2021-08-22      1          45       DE       00+      45
#> 19997:     2021-08-22  2021-08-22      1          45       DE       00+      45
#> 19998:     2021-08-22  2021-08-22      1          45       DE       00+      45
#> 19999:     2021-08-22  2021-08-22      1          45       DE       00+      45
#> 20000:     2021-08-22  2021-08-22      1          45       DE       00+      45
#>        cum_prop_reported delay prop_reported .chain .iteration .draw sample
#>                    <num> <num>         <num>  <int>      <int> <int>  <num>
#>     1:                 1    19             0      1          1     1    149
#>     2:                 1    19             0      1          2     2    149
#>     3:                 1    19             0      1          3     3    149
#>     4:                 1    19             0      1          4     4    149
#>     5:                 1    19             0      1          5     5    149
#>    ---                                                                     
#> 19996:                 1     0             1      2        496   996    232
#> 19997:                 1     0             1      2        497   997    470
#> 19998:                 1     0             1      2        498   998    343
#> 19999:                 1     0             1      2        499   999    436
#> 20000:                 1     0             1      2        500  1000    295