Plot the population posterior prediction for the fraction of samples with the variant of concern

Plot the population posterior prediction for the fraction of samples with the variant of concern

Usage

plot_voc_frac(
  posterior,
  obs = NULL,
  forecast_dates = NULL,
  all_obs = FALSE,
  central = FALSE,
  voc_label = "variant of concern",
  logit = 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.

voc_label

Character string giving the name to assign to the variant of concern. Defaults to "variant of concern".

logit

Logical, defaults to TRUE. Should variant proportions be plot on the logit scale.

...

Additional parameters passed to plot_default().

Value

A ggplot2 plot.

See also

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

Examples

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