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
.check_primarycensored(),
.delay_draw_columns(),
.discretise_parametric_pmf(),
build_ord_obs(),
enw_add_latest_obs_to_nowcast(),
enw_nowcast_samples(),
enw_nowcast_summary(),
enw_posterior(),
enw_posterior_delay(),
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 26.383 25 9.581969
#> 2: 0.4722222 1 12 0.16666667 15.233 15 6.050729
#> 3: 0.5277778 2 4 0.05555556 7.678 7 3.636969
#> 4: 0.5972222 3 5 0.06944444 3.944 4 2.286502
#> 5: 0.5972222 4 0 0.00000000 1.400 1 1.259995
#> ---
#> 606: 0.9298246 1 61 0.35672515 55.768 54 18.172904
#> 607: 1.0000000 2 12 0.07017544 12.969 13 5.157387
#> 608: 0.6160714 0 69 0.61607143 94.223 91 30.188319
#> 609: 1.0000000 1 43 0.38392857 32.499 31 11.903684
#> 610: 1.0000000 0 45 1.00000000 47.577 45 17.455107
#> mad q50 rhat ess_bulk ess_tail
#> <num> <num> <num> <num> <num>
#> 1: 8.8956 25 1.0004729 1061.6093 991.5120
#> 2: 5.9304 15 0.9988477 1023.0243 970.0040
#> 3: 2.9652 7 1.0020368 880.4481 852.4398
#> 4: 2.9652 4 0.9988907 1042.2961 972.7787
#> 5: 1.4826 1 1.0058021 947.5482 928.1070
#> ---
#> 606: 17.7912 54 1.0017605 1121.7985 944.1552
#> 607: 5.9304 13 0.9995106 941.1128 1010.1847
#> 608: 28.1694 91 1.0000863 950.7711 896.0739
#> 609: 10.3782 31 1.0022798 866.9334 748.8873
#> 610: 16.3086 45 1.0013025 1030.5884 807.8255