This function summarises posterior samples for arbitrary strata. It optionally holds out the observed data (variables that are not ".draw", ".iteration", ".sample", ".chain" ) joins this to the summarised posterior.
Arguments
- samples
A
data.frameof posterior samples with at least a numeric sample variable.- 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.
- by
A character vector of variables to summarise by. Defaults to
c("reference_date", ".group").- link_with_obs
Logical, should the observed data be linked to the posterior summary? This is useful for plotting the posterior against the observed data. Defaults to
TRUE.
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_pp_summary(),
enw_quantiles_to_long(),
subset_obs()
Examples
fit <- enw_example("nowcast")
samples <- summary(fit, type = "nowcast_sample")
enw_summarise_samples(samples, probs = c(0.05, 0.5, 0.95))
#> Key: <reference_date, .group>
#> reference_date .group report_date max_confirm location age_group confirm
#> <IDat> <num> <IDat> <int> <fctr> <fctr> <int>
#> 1: 2021-08-03 1 2021-08-22 149 DE 00+ 149
#> 2: 2021-08-04 1 2021-08-22 166 DE 00+ 166
#> 3: 2021-08-05 1 2021-08-22 133 DE 00+ 133
#> 4: 2021-08-06 1 2021-08-22 137 DE 00+ 137
#> 5: 2021-08-07 1 2021-08-22 139 DE 00+ 139
#> 6: 2021-08-08 1 2021-08-22 97 DE 00+ 97
#> 7: 2021-08-09 1 2021-08-22 58 DE 00+ 58
#> 8: 2021-08-10 1 2021-08-22 175 DE 00+ 175
#> 9: 2021-08-11 1 2021-08-22 233 DE 00+ 233
#> 10: 2021-08-12 1 2021-08-22 237 DE 00+ 237
#> 11: 2021-08-13 1 2021-08-22 204 DE 00+ 204
#> 12: 2021-08-14 1 2021-08-22 189 DE 00+ 189
#> 13: 2021-08-15 1 2021-08-22 125 DE 00+ 125
#> 14: 2021-08-16 1 2021-08-22 98 DE 00+ 98
#> 15: 2021-08-17 1 2021-08-22 242 DE 00+ 242
#> 16: 2021-08-18 1 2021-08-22 223 DE 00+ 223
#> 17: 2021-08-19 1 2021-08-22 202 DE 00+ 202
#> 18: 2021-08-20 1 2021-08-22 171 DE 00+ 171
#> 19: 2021-08-21 1 2021-08-22 112 DE 00+ 112
#> 20: 2021-08-22 1 2021-08-22 45 DE 00+ 45
#> reference_date .group report_date max_confirm location age_group confirm
#> <IDat> <num> <IDat> <int> <fctr> <fctr> <int>
#> cum_prop_reported delay prop_reported mean median sd mad
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 1 19 0.000000000 149.000 149 0.000000 0.0000
#> 2: 1 18 0.000000000 167.574 167 1.338774 1.4826
#> 3: 1 17 0.000000000 135.877 136 1.848591 1.4826
#> 4: 1 16 0.000000000 141.495 141 2.425254 2.9652
#> 5: 1 15 0.007194245 146.052 146 2.953645 2.9652
#> 6: 1 14 0.000000000 103.948 104 3.035211 2.9652
#> 7: 1 13 0.000000000 63.054 63 2.460719 2.9652
#> 8: 1 12 0.000000000 185.686 185 3.911356 4.4478
#> 9: 1 11 0.000000000 256.904 257 6.209939 5.9304
#> 10: 1 10 0.004219409 268.527 268 7.155450 7.4130
#> 11: 1 9 0.000000000 237.790 237 7.910656 7.4130
#> 12: 1 8 0.015873016 232.571 232 9.143882 8.8956
#> 13: 1 7 0.040000000 165.001 165 8.814459 8.8956
#> 14: 1 6 0.010204082 129.538 129 7.826993 7.4130
#> 15: 1 5 0.012396694 298.709 298 11.585186 10.3782
#> 16: 1 4 0.017937220 299.200 298 14.635990 14.8260
#> 17: 1 3 0.019801980 300.299 298 19.394632 19.2738
#> 18: 1 2 0.070175439 299.984 298 24.987760 23.7216
#> 19: 1 1 0.383928571 307.161 303 41.407121 41.5128
#> 20: 1 0 1.000000000 319.745 308 79.592443 71.1648
#> cum_prop_reported delay prop_reported mean median sd mad
#> <num> <num> <num> <num> <num> <num> <num>
#> q5 q50 q95
#> <num> <num> <num>
#> 1: 149.00 149 149.0
#> 2: 166.00 167 170.0
#> 3: 133.00 136 139.0
#> 4: 138.00 141 146.0
#> 5: 142.00 146 151.0
#> 6: 100.00 104 109.0
#> 7: 60.00 63 67.0
#> 8: 180.00 185 193.0
#> 9: 247.00 257 268.0
#> 10: 258.00 268 282.0
#> 11: 226.00 237 252.0
#> 12: 218.00 232 248.0
#> 13: 151.00 165 181.0
#> 14: 118.00 129 143.0
#> 15: 281.00 298 318.0
#> 16: 278.00 298 325.0
#> 17: 271.00 298 335.0
#> 18: 262.00 298 342.0
#> 19: 244.95 303 378.1
#> 20: 211.95 308 468.0
#> q5 q50 q95
#> <num> <num> <num>