Loads examples of nowcasts produce 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")
#> obs new_confirm latest
#> 1: <data.table[671x9]> <data.table[630x11]> <data.table[41x10]>
#> missing_reference reporting_triangle metareference
#> 1: <data.table[41x6]> <data.table[41x22]> <data.table[41x9]>
#> metareport metadelay time snapshots by groups max_delay
#> 1: <data.table[60x12]> <data.table[20x4]> 41 41 1 20
#> max_date fit data fit_args samples max_rhat
#> 1: 2021-08-22 <CmdStanMCMC[32]> <list[94]> <list[6]> 1000 1.02
#> divergent_transitions per_divergent_transitions max_treedepth
#> 1: 0 0 8
#> no_at_max_treedepth per_at_max_treedepth run_time
#> 1: 198 0.198 103.8
# Load the preprocessed observations
enw_example(type = "preprocessed_observations")
#> obs new_confirm latest
#> 1: <data.table[671x9]> <data.table[630x11]> <data.table[41x10]>
#> missing_reference reporting_triangle metareference
#> 1: <data.table[41x6]> <data.table[41x22]> <data.table[41x9]>
#> metareport metadelay time snapshots by groups max_delay
#> 1: <data.table[60x12]> <data.table[20x4]> 41 41 1 20
#> max_date
#> 1: 2021-08-22
# Load the latest observations
enw_example(type = "observations")
#> reference_date location age_group confirm report_date
#> 1: 2021-08-02 DE 00+ 59 2021-10-01
#> 2: 2021-08-03 DE 00+ 156 2021-10-01
#> 3: 2021-08-04 DE 00+ 183 2021-10-01
#> 4: 2021-08-05 DE 00+ 147 2021-10-01
#> 5: 2021-08-06 DE 00+ 155 2021-10-01
#> 6: 2021-08-07 DE 00+ 159 2021-10-01
#> 7: 2021-08-08 DE 00+ 119 2021-10-01
#> 8: 2021-08-09 DE 00+ 65 2021-10-01
#> 9: 2021-08-10 DE 00+ 204 2021-10-01
#> 10: 2021-08-11 DE 00+ 275 2021-10-01
#> 11: 2021-08-12 DE 00+ 273 2021-10-01
#> 12: 2021-08-13 DE 00+ 270 2021-10-01
#> 13: 2021-08-14 DE 00+ 262 2021-10-01
#> 14: 2021-08-15 DE 00+ 192 2021-10-01
#> 15: 2021-08-16 DE 00+ 140 2021-10-01
#> 16: 2021-08-17 DE 00+ 323 2021-10-01
#> 17: 2021-08-18 DE 00+ 409 2021-10-01
#> 18: 2021-08-19 DE 00+ 370 2021-10-01
#> 19: 2021-08-20 DE 00+ 361 2021-10-01
#> 20: 2021-08-21 DE 00+ 339 2021-10-01
#> 21: 2021-08-22 DE 00+ 258 2021-10-01
#> reference_date location age_group confirm report_date
# 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 %in% \"00+\"]"
#> [7] "nat_germany_hosp <- enw_filter_report_dates("
#> [8] " nat_germany_hosp,"
#> [9] " latest_date = \"2021-10-01\""
#> [10] ")"
#> [11] ""
#> [12] "# Make sure observations are complete"
#> [13] "nat_germany_hosp <- enw_complete_dates("
#> [14] " nat_germany_hosp,"
#> [15] " by = c(\"location\", \"age_group\")"
#> [16] ")"
#> [17] ""
#> [18] "# Make a retrospective dataset"
#> [19] "retro_nat_germany <- enw_filter_report_dates("
#> [20] " nat_germany_hosp,"
#> [21] " remove_days = 40"
#> [22] ")"
#> [23] "retro_nat_germany <- enw_filter_reference_dates("
#> [24] " retro_nat_germany,"
#> [25] " include_days = 40"
#> [26] ")"
#> [27] ""
#> [28] "# Get latest observations for the same time period"
#> [29] "latest_obs <- enw_latest_data(nat_germany_hosp)"
#> [30] "latest_obs <- enw_filter_reference_dates("
#> [31] " latest_obs,"
#> [32] " remove_days = 40, include_days = 20"
#> [33] ")"
#> [34] ""
#> [35] "# Preprocess observations"
#> [36] "pobs <- enw_preprocess_data(retro_nat_germany, max_delay = 20)"
#> [37] ""
#> [38] "# Reference date model"
#> [39] "reference_module <- enw_reference(~1, data = pobs)"
#> [40] ""
#> [41] "# Report date model"
#> [42] "report_module <- enw_report(~ (1 | day_of_week), data = pobs)"
#> [43] ""
#> [44] "# Compile nowcasting model using multi-threading"
#> [45] "model <- enw_model(threads = TRUE)"
#> [46] ""
#> [47] "# Fit nowcast model and produce a nowcast"
#> [48] "# Note that we have reduced samples for this example to reduce runtimes"
#> [49] "nowcast <- epinowcast(pobs,"
#> [50] " reference = reference_module,"
#> [51] " report = report_module,"
#> [52] " fit = enw_fit_opts("
#> [53] " save_warmup = FALSE, pp = TRUE,"
#> [54] " chains = 2, threads_per_chain = 2,"
#> [55] " iter_warmup = 500, iter_sampling = 500"
#> [56] " ),"
#> [57] " model = model"
#> [58] ")"