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
enw_add_latest_obs_to_nowcast(),
enw_nowcast_samples(),
enw_nowcast_summary(),
enw_posterior(),
enw_pp_summary(),
enw_quantiles_to_long()
Examples
fit <- enw_example("nowcast")
samples <- summary(fit, type = "nowcast_sample")
enw_summarise_samples(samples, probs = c(0.05, 0.5, 0.95))
#> reference_date .group report_date max_confirm location age_group confirm
#> 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
#> cum_prop_reported delay prop_reported mean median sd mad q5
#> 1: 1 19 0.000000000 149.000 149.0 0.000000 0.0000 149
#> 2: 1 18 0.000000000 167.453 167.0 1.291301 1.4826 166
#> 3: 1 17 0.000000000 135.677 135.0 1.853674 1.4826 133
#> 4: 1 16 0.000000000 140.896 141.0 2.169768 2.9652 138
#> 5: 1 15 0.007194245 145.222 145.0 2.760133 2.9652 141
#> 6: 1 14 0.000000000 103.248 103.0 2.893591 2.9652 99
#> 7: 1 13 0.000000000 62.742 62.0 2.412313 2.9652 59
#> 8: 1 12 0.000000000 185.065 185.0 3.687054 4.4478 180
#> 9: 1 11 0.000000000 255.574 255.0 6.079925 5.9304 246
#> 10: 1 10 0.004219409 266.480 266.0 7.480345 7.4130 255
#> 11: 1 9 0.000000000 235.082 235.0 7.671123 7.4130 224
#> 12: 1 8 0.015873016 229.150 229.0 9.532280 10.3782 215
#> 13: 1 7 0.040000000 163.327 163.0 8.941478 8.8956 149
#> 14: 1 6 0.010204082 130.404 130.0 8.343284 8.8956 118
#> 15: 1 5 0.012396694 299.890 299.0 12.795923 13.3434 280
#> 16: 1 4 0.017937220 303.138 301.0 17.375755 17.0499 278
#> 17: 1 3 0.019801980 311.131 309.0 24.503638 23.7216 275
#> 18: 1 2 0.070175439 318.522 315.0 34.923992 34.0998 270
#> 19: 1 1 0.383928571 334.231 327.5 53.967621 51.1497 258
#> 20: 1 0 1.000000000 322.430 306.0 93.868922 80.8017 198
#> q50 q95
#> 1: 149.0 149.00
#> 2: 167.0 170.00
#> 3: 135.0 139.00
#> 4: 141.0 145.00
#> 5: 145.0 150.00
#> 6: 103.0 109.00
#> 7: 62.0 67.00
#> 8: 185.0 191.00
#> 9: 255.0 266.00
#> 10: 266.0 279.05
#> 11: 235.0 248.00
#> 12: 229.0 246.00
#> 13: 163.0 178.00
#> 14: 130.0 145.00
#> 15: 299.0 322.00
#> 16: 301.0 334.05
#> 17: 309.0 356.00
#> 18: 315.0 383.00
#> 19: 327.5 436.00
#> 20: 306.0 493.05