Loads examples of nowcasts produced using example scripts. Used to streamline
examples, in package tests and to enable users to explore package
functionality without needing to install cmdstanr.
Usage
enw_example(
type = c("nowcast", "preprocessed_observations", "observations", "script")
)Arguments
- type
A character string indicating the example to load. Supported options are
"nowcast", for
epinowcast()applied to germany_covid19_hosp"preprocessed_observations", for
enw_preprocess_data()applied to germany_covid19_hosp"observations", for
enw_latest_data()applied to germany_covid19_hosp"script", the code used to generate these examples.
Value
Depending on type, a data.table of the requested output OR
the file name(s) to generate these outputs (type = "script")
See also
Package data sets
germany_covid19_hosp
Examples
# Load the nowcast
enw_example(type = "nowcast")
#> ── epinowcast model output ─────────────────────────────────────────────────────
#> Groups: 1 | Timestep: day | Max delay: 20
#> Observations: 40 timepoints x 40 snapshots
#> Max date: 2021-08-22
#>
#> Datasets (access with `enw_get_data(x, "<name>")`):
#> obs : 650 x 9
#> new_confirm : 610 x 11
#> latest : 40 x 10
#> missing_reference : 40 x 6
#> reporting_triangle : 40 x 22
#> metareference : 40 x 9
#> metareport : 59 x 12
#> metadelay : 20 x 5
#>
#> Model objects (access with `enw_get_data(x, "<name>")`):
#> priors : 14 x 6
#> fit : CmdStanMCMC
#> data : list(112)
#> fit_args : list(5)
#> init_method_output : NULL
#> Model fit:
#> Samples: 1,000 | Max Rhat: 1.01
#> Divergent transitions: 0 (0%)
#> Max treedepth: 8 (3 at max, 0.3%)
#> Run time: 26 secs
# Load the preprocessed observations
enw_example(type = "preprocessed_observations")
#> ── Preprocessed nowcast data ───────────────────────────────────────────────────
#> Groups: 1 | Timestep: day | Max delay: 20
#> Observations: 40 timepoints x 40 snapshots
#> Max date: 2021-08-22
#>
#> Datasets (access with `enw_get_data(x, "<name>")`):
#> obs : 650 x 9
#> new_confirm : 610 x 11
#> latest : 40 x 10
#> missing_reference : 40 x 6
#> reporting_triangle : 40 x 22
#> metareference : 40 x 9
#> metareport : 59 x 12
#> metadelay : 20 x 5
# Load the latest observations
enw_example(type = "observations")
#> reference_date location age_group report_date confirm
#> <IDat> <fctr> <fctr> <IDat> <int>
#> 1: 2021-08-03 DE 00+ 2021-10-01 156
#> 2: 2021-08-04 DE 00+ 2021-10-01 183
#> 3: 2021-08-05 DE 00+ 2021-10-01 147
#> 4: 2021-08-06 DE 00+ 2021-10-01 155
#> 5: 2021-08-07 DE 00+ 2021-10-01 159
#> 6: 2021-08-08 DE 00+ 2021-10-01 119
#> 7: 2021-08-09 DE 00+ 2021-10-01 65
#> 8: 2021-08-10 DE 00+ 2021-10-01 204
#> 9: 2021-08-11 DE 00+ 2021-10-01 275
#> 10: 2021-08-12 DE 00+ 2021-10-01 273
#> 11: 2021-08-13 DE 00+ 2021-10-01 270
#> 12: 2021-08-14 DE 00+ 2021-10-01 262
#> 13: 2021-08-15 DE 00+ 2021-10-01 192
#> 14: 2021-08-16 DE 00+ 2021-10-01 140
#> 15: 2021-08-17 DE 00+ 2021-10-01 323
#> 16: 2021-08-18 DE 00+ 2021-10-01 409
#> 17: 2021-08-19 DE 00+ 2021-10-01 370
#> 18: 2021-08-20 DE 00+ 2021-10-01 361
#> 19: 2021-08-21 DE 00+ 2021-10-01 339
#> 20: 2021-08-22 DE 00+ 2021-10-01 258
#> reference_date location age_group report_date confirm
#> <IDat> <fctr> <fctr> <IDat> <int>
# Load the script used to generate these examples
# Optionally source this script to regenerate the example
readLines(enw_example(type = "script"))
#> [1] "# Load epinowcast and data.table"
#> [2] "library(epinowcast)"
#> [3] "library(data.table)"
#> [4] ""
#> [5] "# Load and filter germany hospitalisations"
#> [6] "nat_germany_hosp <- germany_covid19_hosp[location == \"DE\"][age_group == \"00+\"]"
#> [7] "nat_germany_hosp <- enw_filter_report_dates("
#> [8] " nat_germany_hosp, latest_date = \"2021-10-01\""
#> [9] ")"
#> [10] ""
#> [11] "# Make sure observations are complete"
#> [12] "nat_germany_hosp <- enw_complete_dates("
#> [13] " nat_germany_hosp, by = c(\"location\", \"age_group\")"
#> [14] ")"
#> [15] ""
#> [16] "# Make a retrospective dataset"
#> [17] "retro_nat_germany <- enw_filter_report_dates("
#> [18] " nat_germany_hosp, remove_days = 40"
#> [19] ")"
#> [20] "retro_nat_germany <- enw_filter_reference_dates("
#> [21] " retro_nat_germany, include_days = 40"
#> [22] ")"
#> [23] ""
#> [24] "# Get latest observations for the same time period"
#> [25] "latest_obs <- nat_germany_hosp |>"
#> [26] " enw_obs_at_delay(max_delay = 20) |>"
#> [27] " enw_filter_reference_dates("
#> [28] " remove_days = 40, include_days = 20"
#> [29] " )"
#> [30] ""
#> [31] "# Preprocess observations"
#> [32] "pobs <- enw_preprocess_data(retro_nat_germany, max_delay = 20)"
#> [33] ""
#> [34] "# Reference date model"
#> [35] "reference_module <- enw_reference(~1, data = pobs)"
#> [36] ""
#> [37] "# Report date model"
#> [38] "report_module <- enw_report(~ (1 | day_of_week), data = pobs)"
#> [39] ""
#> [40] "# Fit nowcast model and produce a nowcast"
#> [41] "# Note that we have reduced samples for this example to reduce runtimes"
#> [42] "nowcast <- epinowcast(pobs,"
#> [43] " reference = reference_module,"
#> [44] " report = report_module,"
#> [45] " fit = enw_fit_opts("
#> [46] " save_warmup = FALSE, pp = TRUE,"
#> [47] " chains = 2, threads_per_chain = 2,"
#> [48] " iter_warmup = 500, iter_sampling = 500"
#> [49] " )"
#> [50] ")"