Summary plots to compare timeseries and forecast models

Usage

plot_compare_timeseries(
  compare_timeseries_output,
  type = c("summary_score", "horizon_score", "region_score"),
  score = c("Bias", "CRPS", "Dispersion", "AE (median)", "SE (mean)")
)

Arguments

compare_timeseries_output: A named list of dataframes produced by compare_timeseries
type: Type(s) of summary plot to be produced for Rt and case observations for each model in n compare_timeseries_output. "summary_score" provides a plot of model fit scores for the 0-7 and 8-14 day horizons. If desired, a subset of scores can be specified using the score argument. "horizon_score" provides a plot of scores (CRPS, Calibration, Sharpness, Median, IQR, CI, Bias) across horizons. "region_score" provides a plot of scores (CRPS, Calibration, Sharpness, Bias, Median, IQR) by region for the 0-7 and 8-14 day horizons.
score: (Optional) One or more of c("Bias","CRPS","Sharpness","Calibration","Median","IQR","CI") when type="summary_score" is used.

Value

A named list of ggplot2 objects

Examples

if (FALSE) {
obs_rts <- EpiSoon::example_obs_rts %>%
  dplyr::mutate(timeseries = "Region 1") %>%
  dplyr::bind_rows(EpiSoon::example_obs_rts %>%
    dplyr::mutate(timeseries = "Region 2"))

obs_cases <- EpiSoon::example_obs_cases %>%
  dplyr::mutate(timeseries = "Region 1") %>%
  dplyr::bind_rows(EpiSoon::example_obs_cases %>%
    dplyr::mutate(timeseries = "Region 2"))

models <- list(
  "AR 3" = function(...) {
    EpiSoon::bsts_model(model = function(ss, y) {
      bsts::AddAr(ss, y = y, lags = 3)
    }, ...)
  },
  "Semi-local linear trend" = function(...) {
    EpiSoon::bsts_model(model = function(ss, y) {
      bsts::AddSemilocalLinearTrend(ss, y = y)
    }, ...)
  }
)

forecast_eval <-
  compare_timeseries(obs_rts, obs_cases, models,
    horizon = 10, samples = 10,
    serial_interval = EpiSoon::example_serial_interval
  )

## Produce all plots
plot_compare_timeseries(forecast_eval)

## Produce subsets of plots
plot_compare_timeseries(forecast_eval, type = "summary_score")
plot_compare_timeseries(forecast_eval,
  type = "summary_score",
  score = "Bias"
)
plot_compare_timeseries(forecast_eval, type = "horizon_score")
plot_compare_timeseries(forecast_eval, type = "region_score")
plot_compare_timeseries(forecast_eval,
  type = c("horizon_score", "region_score")
)
}