forecast_across_scenarios: Forecast across multiple scenarios and dates

In epiforecasts/forecast.vocs: Forecast Case and Sequence Notifications using Variant of Concern Strain Dynamics

Forecast across multiple scenarios and dates

Description

Forecast across multiple scenarios and dates

Usage

forecast_across_scenarios(obs, scenarios, ...)

Arguments

obs	A data.frame with the following variables: date, cases, seq_voc, and seq_total, cases_available, and seq_available. seq_available and case_available must be uniquely define data rows but other rows can be duplicated based on data availability. This data format allows for multiple versions of case and sequence data for a given date with different reporting dates. This is important when using the package in evaluation settings or in real-time where data sources are liable to be updated as new data becomes available. See germany_covid19_delta_obs for an example of a supported data set.
scenarios	A data.frame of scenarios as produced by define_scenarios(). If an obs variable is present this is used as the scenario data but otherwise generate_obs_scenario() is used to generate this data from the other variables in scenarios.
...	Additional parameters passed to forecast_across_dates().

Value

A data table each rows containing the output from running forecast() on a single scenario for a single forecast date.

See Also

Functions used for forecasting across models, dates, and scenarios forecast_across_dates(), forecast_n_strain(), forecast(), plot.fv_forecast(), summary.fv_forecast(), unnest_posterior()

Examples

library(ggplot2)
options(mc.cores = 4)

scenarios <- define_scenarios(
  voc_scale = list(c(0, 0.5), c(0.5, 0.25)),
  seq_lag = 1,
  seq_samples = 1
)
scenarios

forecasts <- forecast_across_scenarios(
  germany_covid19_delta_obs,
  scenarios,
  forecast_dates = c(as.Date("2021-05-01"), as.Date("2021-06-12")),
  horizon = 4,
  strains = 2,
  adapt_delta = 0.99,
  max_treedepth = 15,
  variant_relationship = "scaled"
)

# inspect forecasts
forecasts

# unnest posteriors
posteriors <- unnest_posterior(forecasts)

# plot case posterior predictions
plot_cases(posteriors, log = TRUE) +
  facet_grid(vars(forecast_date))

epiforecasts/forecast.vocs documentation built on May 14, 2023, 2 p.m.