This function summarises posterior predictives
for observed data (by report and reference date). The functionality of
this function can be used directly on the output of epinowcast() using
the supplied summary.epinowcast() method.
Usage
enw_pp_summary(fit, diff_obs, probs = c(0.05, 0.2, 0.35, 0.5, 0.65, 0.8, 0.95))Arguments
- fit
A
cmdstanrfit object.- diff_obs
A
data.frameof observed data with at least a date variablereference_date, and a grouping variable.group.- probs
A vector of numeric probabilities to produce quantile summaries for. By default these are the 5%, 20%, 80%, and 95% quantiles which are also the minimum set required for plotting functions to work.
See also
Functions used for postprocessing of model fits
build_ord_obs(),
enw_add_latest_obs_to_nowcast(),
enw_nowcast_samples(),
enw_nowcast_summary(),
enw_posterior(),
enw_quantiles_to_long(),
enw_summarise_samples(),
subset_obs()
Examples
fit <- enw_example("nowcast")
enw_pp_summary(fit$fit[[1]], fit$new_confirm[[1]], probs = c(0.5))
#> reference_date report_date .group max_confirm location age_group confirm
#> <IDat> <IDat> <num> <int> <fctr> <fctr> <int>
#> 1: 2021-07-14 2021-07-14 1 72 DE 00+ 22
#> 2: 2021-07-14 2021-07-15 1 72 DE 00+ 34
#> 3: 2021-07-14 2021-07-16 1 72 DE 00+ 38
#> 4: 2021-07-14 2021-07-17 1 72 DE 00+ 43
#> 5: 2021-07-14 2021-07-18 1 72 DE 00+ 43
#> ---
#> 606: 2021-08-20 2021-08-21 1 171 DE 00+ 159
#> 607: 2021-08-20 2021-08-22 1 171 DE 00+ 171
#> 608: 2021-08-21 2021-08-21 1 112 DE 00+ 69
#> 609: 2021-08-21 2021-08-22 1 112 DE 00+ 112
#> 610: 2021-08-22 2021-08-22 1 45 DE 00+ 45
#> cum_prop_reported delay new_confirm prop_reported mean median sd
#> <num> <num> <int> <num> <num> <num> <num>
#> 1: 0.3055556 0 22 0.30555556 26.163 25 9.344932
#> 2: 0.4722222 1 12 0.16666667 15.230 14 5.883852
#> 3: 0.5277778 2 4 0.05555556 7.573 7 3.420581
#> 4: 0.5972222 3 5 0.06944444 3.982 4 2.336479
#> 5: 0.5972222 4 0 0.00000000 1.432 1 1.253374
#> ---
#> 606: 0.9298246 1 61 0.35672515 55.377 54 18.115492
#> 607: 1.0000000 2 12 0.07017544 13.307 13 5.440437
#> 608: 0.6160714 0 69 0.61607143 92.551 88 31.907107
#> 609: 1.0000000 1 43 0.38392857 32.052 31 11.525630
#> 610: 1.0000000 0 45 1.00000000 46.813 44 18.391745
#> mad q50 rhat ess_bulk ess_tail
#> <num> <num> <num> <num> <num>
#> 1: 8.8956 25 1.0043573 944.5563 985.9832
#> 2: 5.9304 14 1.0014240 1000.5986 911.2469
#> 3: 2.9652 7 0.9993039 1070.3435 922.9781
#> 4: 2.9652 4 1.0012548 817.6990 911.8348
#> 5: 1.4826 1 0.9990018 964.9174 860.7339
#> ---
#> 606: 17.7912 54 1.0010789 1038.1755 1067.1632
#> 607: 5.9304 13 0.9999275 993.4925 998.6745
#> 608: 29.6520 88 0.9999278 1097.1067 981.4012
#> 609: 10.3782 31 1.0024538 928.9540 888.5787
#> 610: 16.3086 44 1.0029994 1083.9580 865.5026