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")
#> obs new_confirm latest
#> <list> <list> <list>
#> 1: <data.table[671x9]> <data.table[630x11]> <data.table[41x10]>
#> missing_reference reporting_triangle metareference
#> <list> <list> <list>
#> 1: <data.table[41x6]> <data.table[41x22]> <data.table[41x9]>
#> metareport metadelay max_delay time snapshots by
#> <list> <list> <num> <int> <int> <list>
#> 1: <data.table[60x12]> <data.table[20x5]> 20 41 41
#> groups max_date timestep priors
#> <int> <IDat> <char> <list>
#> 1: 1 2021-08-22 day <data.table[14x6]>
#> fit
#> <list>
#> 1: <CmdStanMCMC>\n Inherits from: <CmdStanFit>\n Public:\n clone: function (deep = FALSE) \n cmdstan_diagnose: function () \n cmdstan_summary: function (flags = NULL) \n code: function () \n constrain_variables: function (unconstrained_variables, transformed_parameters = TRUE, \n data_file: function () \n diagnostic_summary: function (diagnostics = c("divergences", "treedepth", "ebfmi"), \n draws: function (variables = NULL, inc_warmup = FALSE, format = getOption("cmdstanr_draws_format", \n expose_functions: function (global = FALSE, verbose = FALSE) \n functions: environment\n grad_log_prob: function (unconstrained_variables, jacobian_adjustment = TRUE) \n hessian: function (unconstrained_variables, jacobian_adjustment = TRUE) \n init: function () \n init_model_methods: function (seed = 0, verbose = FALSE, hessian = FALSE) \n initialize: function (runset) \n inv_metric: function (matrix = TRUE) \n latent_dynamics_files: function (include_failed = FALSE) \n log_prob: function (unconstrained_variables, jacobian_adjustment = TRUE) \n loo: function (variables = "log_lik", r_eff = TRUE, moment_match = FALSE, \n lp: function () \n metadata: function () \n num_chains: function () \n num_procs: function () \n output: function (id = NULL) \n output_files: function (include_failed = FALSE) \n print: function (variables = NULL, ..., digits = 2, max_rows = getOption("cmdstanr_max_rows", \n profile_files: function (include_failed = FALSE) \n profiles: function () \n return_codes: function () \n runset: CmdStanRun, R6\n sampler_diagnostics: function (inc_warmup = FALSE, format = getOption("cmdstanr_draws_format", \n save_data_file: function (dir = ".", basename = NULL, timestamp = TRUE, random = TRUE) \n save_latent_dynamics_files: function (dir = ".", basename = NULL, timestamp = TRUE, random = TRUE) \n save_object: function (file, ...) \n save_output_files: function (dir = ".", basename = NULL, timestamp = TRUE, random = TRUE) \n save_profile_files: function (dir = ".", basename = NULL, timestamp = TRUE, random = TRUE) \n summary: function (variables = NULL, ...) \n time: function () \n unconstrain_draws: function (files = NULL, draws = NULL) \n unconstrain_variables: function (variables) \n variable_skeleton: function (transformed_parameters = TRUE, generated_quantities = TRUE) \n Private:\n draws_: -1371.04 -1377.39 -1378.06 -1383.26 -1375.59 -1378.01 -1 ...\n init_: NULL\n inv_metric_: list\n metadata_: list\n model_methods_env_: environment\n profiles_: NULL\n read_csv_: function (variables = NULL, sampler_diagnostics = NULL, format = getOption("cmdstanr_draws_format", \n sampler_diagnostics_: 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 ...\n warmup_draws_: NULL\n warmup_sampler_diagnostics_: NULL
#> data fit_args samples max_rhat divergent_transitions
#> <list> <list> <int> <num> <num>
#> 1: <list[116]> <list[6]> 1000 1.02 0
#> per_divergent_transitions max_treedepth no_at_max_treedepth
#> <num> <num> <int>
#> 1: 0 7 993
#> per_at_max_treedepth run_time
#> <num> <num>
#> 1: 0.993 70.6
# Load the preprocessed observations
enw_example(type = "preprocessed_observations")
#> obs new_confirm latest
#> <list> <list> <list>
#> 1: <data.table[671x9]> <data.table[630x11]> <data.table[41x10]>
#> missing_reference reporting_triangle metareference
#> <list> <list> <list>
#> 1: <data.table[41x6]> <data.table[41x22]> <data.table[41x9]>
#> metareport metadelay max_delay time snapshots by
#> <list> <list> <num> <int> <int> <list>
#> 1: <data.table[60x12]> <data.table[20x5]> 20 41 41
#> groups max_date timestep
#> <int> <IDat> <char>
#> 1: 1 2021-08-22 day
# Load the latest observations
enw_example(type = "observations")
#> reference_date location age_group report_date confirm
#> <IDat> <fctr> <fctr> <IDat> <int>
#> 1: 2021-08-02 DE 00+ 2021-10-01 59
#> 2: 2021-08-03 DE 00+ 2021-10-01 156
#> 3: 2021-08-04 DE 00+ 2021-10-01 183
#> 4: 2021-08-05 DE 00+ 2021-10-01 147
#> 5: 2021-08-06 DE 00+ 2021-10-01 155
#> 6: 2021-08-07 DE 00+ 2021-10-01 159
#> 7: 2021-08-08 DE 00+ 2021-10-01 119
#> 8: 2021-08-09 DE 00+ 2021-10-01 65
#> 9: 2021-08-10 DE 00+ 2021-10-01 204
#> 10: 2021-08-11 DE 00+ 2021-10-01 275
#> 11: 2021-08-12 DE 00+ 2021-10-01 273
#> 12: 2021-08-13 DE 00+ 2021-10-01 270
#> 13: 2021-08-14 DE 00+ 2021-10-01 262
#> 14: 2021-08-15 DE 00+ 2021-10-01 192
#> 15: 2021-08-16 DE 00+ 2021-10-01 140
#> 16: 2021-08-17 DE 00+ 2021-10-01 323
#> 17: 2021-08-18 DE 00+ 2021-10-01 409
#> 18: 2021-08-19 DE 00+ 2021-10-01 370
#> 19: 2021-08-20 DE 00+ 2021-10-01 361
#> 20: 2021-08-21 DE 00+ 2021-10-01 339
#> 21: 2021-08-22 DE 00+ 2021-10-01 258
#> reference_date location age_group report_date confirm
# 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 <- enw_latest_data(nat_germany_hosp)"
#> [26] "latest_obs <- enw_filter_reference_dates("
#> [27] " latest_obs, remove_days = 40, include_days = 20"
#> [28] ")"
#> [29] ""
#> [30] "# Preprocess observations"
#> [31] "pobs <- enw_preprocess_data(retro_nat_germany, max_delay = 20)"
#> [32] ""
#> [33] "# Reference date model"
#> [34] "reference_module <- enw_reference(~1, data = pobs)"
#> [35] ""
#> [36] "# Report date model"
#> [37] "report_module <- enw_report(~ (1 | day_of_week), data = pobs)"
#> [38] ""
#> [39] "# Fit nowcast model and produce a nowcast"
#> [40] "# Note that we have reduced samples for this example to reduce runtimes"
#> [41] "nowcast <- epinowcast(pobs,"
#> [42] " reference = reference_module,"
#> [43] " report = report_module,"
#> [44] " fit = enw_fit_opts("
#> [45] " save_warmup = FALSE, pp = TRUE,"
#> [46] " chains = 2, threads_per_chain = 2,"
#> [47] " iter_warmup = 500, iter_sampling = 500"
#> [48] " )"
#> [49] ")"