plot_forecast: Plot forecasts and optional truth for only one selected...
In reichlab/covidHubUtils: Utility functions for the COVID-19 forecast hub

plot_forecast

R Documentation

Plot forecasts and optional truth for only one selected target variable. Faceted plots for multiple models, locations and forecast dates are supported with specified facet formula.

Description

\Sexpr[results=rd, stage=render]{lifecycle::badge("deprecated")}

Please use plot_forecasts() instead.

Usage

plot_forecast(
  forecast_data,
  truth_data = NULL,
  hub = c("US", "ECDC", "FluSight"),
  models = NULL,
  target_variable,
  locations = NULL,
  facet = NULL,
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  forecast_dates = NULL,
  intervals,
  horizon,
  truth_source,
  use_median_as_point = FALSE,
  plot_truth = TRUE,
  plot = TRUE,
  fill_by_model = FALSE,
  fill_transparency = 1,
  truth_as_of = NULL,
  title = "default",
  subtitle = "default",
  show_caption = TRUE
)

Arguments

`forecast_data`	required data.frame with forecasts in the format returned by `load_forecasts()`
`truth_data`	optional data.frame from one truth source in the format returned by `load_truth()`. It needs to have columns `model`, `target_variable`, `target_end_date`, `⁠location and value⁠`. `Model` column can be `"Observed Data (a truth source)"`.
`hub`	character vector, where the first element indicates the hub from which to load forecasts. Possible options are `"US"`, `"ECDC"` and `"FluSight"`.
`models`	vector of strings specifying models to plot. Default to all models in `forecast_data`.
`target_variable`	string specifying target type. It should be one of `"cum death"`, `"inc case"`, `"inc death"`, `"inc hosp"` and `"inc flu hosp"`. `"cum death"` and `"inc hosp"` are only available in forecasts from US hub now. If there is only one `target_variable` in `forecast_data`, this parameter is optional.
`locations`	a vector of strings of fips code or CBSA codes or location names, such as "Hampshire County, MA", "Alabama", "United Kingdom". A US county location names must include state abbreviation. Default to `NULL` which would include all locations in `forecast_data`.
`facet`	interpretable facet option for ggplot. Function will error if multiple locations are passed in without location in the facet formula.
`facet_scales`	argument for scales in ggplot2::facet_wrap. Default to `"fixed"`.
`facet_nrow`	number of rows for facetting; optional.
`facet_ncol`	number of columns for facetting; optional.
`forecast_dates`	date string vectors for forecast dates to plot. Default to forecast_dates present in the data.
`intervals`	values indicating which central prediction interval levels to plot. `NULL` means only plotting point forecasts. If not provided, it will default to `c(.5, .8, .95)`. When plotting 6 models or more, the plot will be reduced to show .95 interval only.
`horizon`	forecasts are plotted for the horizon time steps after the forecast date. Default to all available horizons in `forecast_data`.
`truth_source`	character specifying where the truth data will be loaded from if `truth_data` is not provided. Currently support `"JHU"`, `"NYTimes"`, `"HealthData"` and `"ECDC"`. Optional if `truth_data` is provided.
`use_median_as_point`	logical for using median quantiles as point forecasts in plot. Default to `FALSE`.
`plot_truth`	logical for showing truth data in plot. Default to `TRUE`. Data used in the plot is either `truth_data` or data loaded from `truth_source`.
`plot`	logical for showing the plot. Default to `TRUE`.
`fill_by_model`	logical for specifying colors in plot. If `TRUE`, separate colors will be used for each model. If `FALSE`, only blues will be used for all models. Default to `FALSE`.
`fill_transparency`	numeric value used to set transparency of intervals. 0 means fully transparent, 1 means opaque.
`truth_as_of`	the plot includes the truth data that would have been in real time as of the `truth_as_of` date (not using this parameter when truth data is from github repo)
`title`	optional text for the title of the plot. If left as `"default"`, the title will be automatically generated. If `"none"`, no title will be plotted.
`subtitle`	optional text for the subtitle of the plot. If left as `"default"`, the subtitle will be automatically generated. If `"none"`, no subtitle will be plotted.
`show_caption`	logical, if `TRUE`, caption will be included showing data sources