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.frame
of 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