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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)

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().

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 enw_add_latest_obs_to_nowcast(), enw_nowcast_summary(), enw_posterior(), enw_pp_summary(), enw_quantiles_to_long(), enw_summarise_samples()

Examples

fit <- enw_example("nowcast")
enw_nowcast_samples(fit$fit[[1]], fit$latest[[1]])
#>        reference_date report_date .group max_confirm location age_group confirm
#>     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
#>     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    409
#> 19997:                 1     0             1      2        497   997    362
#> 19998:                 1     0             1      2        498   998    272
#> 19999:                 1     0             1      2        499   999    247
#> 20000:                 1     0             1      2        500  1000    189