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
#> 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 167.426 167 1.316912 1.4826
#> 3: 1 17 0.000000000 135.812 136 1.867121 1.4826
#> 4: 1 16 0.000000000 141.255 141 2.341679 2.2239
#> 5: 1 15 0.007194245 145.884 146 3.085460 2.9652
#> 6: 1 14 0.000000000 103.681 103 3.072243 2.9652
#> 7: 1 13 0.000000000 62.762 62 2.461588 1.4826
#> 8: 1 12 0.000000000 185.138 185 3.827742 4.4478
#> 9: 1 11 0.000000000 255.903 255 6.410514 5.9304
#> 10: 1 10 0.004219409 267.488 267 7.975931 7.4130
#> 11: 1 9 0.000000000 236.164 236 8.459235 8.8956
#> 12: 1 8 0.015873016 230.867 230 10.092332 10.3782
#> 13: 1 7 0.040000000 165.026 165 10.254095 10.3782
#> 14: 1 6 0.010204082 129.307 128 8.532969 8.8956
#> 15: 1 5 0.012396694 292.749 292 11.792076 11.8608
#> 16: 1 4 0.017937220 293.296 292 15.992941 14.8260
#> 17: 1 3 0.019801980 291.404 290 19.436887 19.2738
#> 18: 1 2 0.070175439 295.703 292 28.861250 28.1694
#> 19: 1 1 0.383928571 309.456 304 51.295236 47.4432
#> 20: 1 0 1.000000000 381.243 371 103.890978 96.3690
#> cum_prop_reported delay prop_reported mean median sd mad
#> q5 q50 q95
#> <num> <num> <num>
#> 1: 149.00 149 149.00
#> 2: 166.00 167 170.00
#> 3: 133.00 136 139.00
#> 4: 138.00 141 145.00
#> 5: 141.00 146 151.05
#> 6: 99.00 103 109.00
#> 7: 59.00 62 67.00
#> 8: 180.00 185 192.00
#> 9: 246.00 255 267.00
#> 10: 255.00 267 281.00
#> 11: 223.00 236 252.00
#> 12: 216.00 230 249.00
#> 13: 149.95 165 183.00
#> 14: 116.00 128 144.05
#> 15: 275.00 292 313.00
#> 16: 270.00 292 320.00
#> 17: 263.00 290 325.00
#> 18: 254.95 292 348.00
#> 19: 237.00 304 406.00
#> 20: 240.85 371 569.05
#> q5 q50 q95