Plot the posterior prediction for cases

Plot the posterior prediction for cases

Usage

plot_cases(
  posterior,
  obs = NULL,
  forecast_dates = NULL,
  all_obs = FALSE,
  central = FALSE,
  col = NULL,
  log = TRUE
)

Arguments

posterior

A dataframe of posterior output as produced by fv_tidy_posterior(). For forecast dates to be extracted data with value_type == "cases" must be present.

obs

A data frame of observed data as produced by latest_obs().

forecast_dates

A data.frame in the format produced by extract_forecast_dates() (with at least a date variable and a Data unavailable variable)). Specifies when date availability should be add to plots. May contain faceting variables.

all_obs

Logical, defaults to FALSE. Should all observations be plot or just those in the date range of the estimates being plot.

central

Logical, defaults to FALSE. Should the mean and median central estimates be plot as dashed and solid lines respectively. Requires mean and median variables to be present in the input.

col

A character string denoting the variable to use to stratify the ribbon plot. Defaults to "type" which indicates the data stream.

log

Logical, defaults to TRUE. Should cases be plot on the log 2 scale?

Value

A ggplot2 plot.

See also

Plotting functions add_forecast_dates(), plot.fv_forecast(), plot.fv_posterior(), plot_default(), plot_growth(), plot_pairs(), plot_posterior(), plot_rt(), plot_theme(), plot_voc_advantage(), plot_voc_frac(), save_plots()

Examples

posterior <- fv_example(strains = 2, type = "posterior")

# default with log transform
plot_cases(posterior)


# without log transform
plot_cases(posterior, log = FALSE)