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
.check_primarycensored(),
.delay_draw_columns(),
.discretise_parametric_pmf(),
build_ord_obs(),
enw_add_latest_obs_to_nowcast(),
enw_nowcast_samples(),
enw_nowcast_summary(),
enw_posterior(),
enw_posterior_delay(),
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 0.000000 0.0000
#> 2: 1 18 0.000000000 167.570 167.0 1.341976 1.4826
#> 3: 1 17 0.000000000 135.841 136.0 1.839865 1.4826
#> 4: 1 16 0.000000000 141.576 141.0 2.333167 2.9652
#> 5: 1 15 0.007194245 146.294 146.0 2.986383 2.9652
#> 6: 1 14 0.000000000 104.040 104.0 3.024822 2.9652
#> 7: 1 13 0.000000000 62.986 63.0 2.453125 2.9652
#> 8: 1 12 0.000000000 185.872 186.0 3.783640 4.4478
#> 9: 1 11 0.000000000 257.301 257.0 6.031150 5.9304
#> 10: 1 10 0.004219409 268.618 268.0 7.433797 7.4130
#> 11: 1 9 0.000000000 237.750 237.0 7.647090 7.4130
#> 12: 1 8 0.015873016 232.124 231.0 9.302750 8.8956
#> 13: 1 7 0.040000000 164.968 164.0 8.833516 8.8956
#> 14: 1 6 0.010204082 129.748 129.0 7.402790 7.4130
#> 15: 1 5 0.012396694 298.836 298.0 11.534477 10.3782
#> 16: 1 4 0.017937220 299.495 299.0 15.778623 16.3086
#> 17: 1 3 0.019801980 300.872 299.0 19.534206 17.7912
#> 18: 1 2 0.070175439 301.149 299.5 25.061901 25.9455
#> 19: 1 1 0.383928571 310.948 304.5 44.585526 40.7715
#> 20: 1 0 1.000000000 322.429 310.5 77.062219 71.9061
#> cum_prop_reported delay prop_reported mean median sd mad
#> <num> <num> <num> <num> <num> <num> <num>
#> q5 q50 q95
#> <num> <num> <num>
#> 1: 149.00 149.0 149.00
#> 2: 166.00 167.0 170.00
#> 3: 133.00 136.0 139.00
#> 4: 138.00 141.0 146.00
#> 5: 142.00 146.0 151.00
#> 6: 99.95 104.0 109.00
#> 7: 60.00 63.0 67.00
#> 8: 180.00 186.0 192.00
#> 9: 248.00 257.0 267.00
#> 10: 257.00 268.0 281.05
#> 11: 226.00 237.0 251.05
#> 12: 218.00 231.0 249.00
#> 13: 152.00 164.0 180.05
#> 14: 118.00 129.0 143.00
#> 15: 282.00 298.0 319.05
#> 16: 275.00 299.0 328.00
#> 17: 272.00 299.0 334.05
#> 18: 263.00 299.5 347.00
#> 19: 250.00 304.5 396.00
#> 20: 214.95 310.5 463.10
#> q5 q50 q95
#> <num> <num> <num>