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 0.000000 0.0000
#> 2: 1 18 0.000000000 167.480 167.0 1.403414 1.4826
#> 3: 1 17 0.000000000 135.797 136.0 1.858291 1.4826
#> 4: 1 16 0.000000000 141.272 141.0 2.414507 2.9652
#> 5: 1 15 0.007194245 145.764 145.0 3.070461 2.9652
#> 6: 1 14 0.000000000 103.614 103.0 2.892987 2.9652
#> 7: 1 13 0.000000000 62.838 63.0 2.595475 2.9652
#> 8: 1 12 0.000000000 185.149 185.0 3.655155 2.9652
#> 9: 1 11 0.000000000 256.191 256.0 7.084540 7.4130
#> 10: 1 10 0.004219409 267.189 266.0 8.269563 7.4130
#> 11: 1 9 0.000000000 236.218 235.0 8.635453 8.8956
#> 12: 1 8 0.015873016 230.463 230.0 10.395995 10.3782
#> 13: 1 7 0.040000000 165.184 165.0 9.660925 8.8956
#> 14: 1 6 0.010204082 129.535 129.0 8.499354 8.8956
#> 15: 1 5 0.012396694 293.236 292.0 11.922603 11.8608
#> 16: 1 4 0.017937220 293.392 292.0 15.981231 14.8260
#> 17: 1 3 0.019801980 291.537 290.0 20.271200 20.7564
#> 18: 1 2 0.070175439 295.258 292.5 29.356997 27.4281
#> 19: 1 1 0.383928571 310.440 304.0 50.020660 47.4432
#> 20: 1 0 1.000000000 384.142 368.0 115.713601 97.8516
#> cum_prop_reported delay prop_reported mean median sd mad
#> q5 q50 q95
#> <num> <num> <num>
#> 1: 149.00 149.0 149.00
#> 2: 166.00 167.0 170.00
#> 3: 133.00 136.0 139.00
#> 4: 138.00 141.0 146.00
#> 5: 141.00 145.0 151.00
#> 6: 99.00 103.0 109.00
#> 7: 59.00 63.0 68.00
#> 8: 180.00 185.0 192.00
#> 9: 246.00 256.0 269.00
#> 10: 255.00 266.0 282.00
#> 11: 224.00 235.0 252.00
#> 12: 215.00 230.0 249.00
#> 13: 150.00 165.0 182.00
#> 14: 117.00 129.0 144.00
#> 15: 276.00 292.0 315.00
#> 16: 269.00 292.0 321.00
#> 17: 262.00 290.0 327.05
#> 18: 252.00 292.5 350.00
#> 19: 238.95 304.0 396.10
#> 20: 235.00 368.0 602.00
#> q5 q50 q95