Plot a SEIR model projection

plot_projection(
  pred_dat,
  obs_dat,
  col = "#377EB8",
  value_column = "value",
  date_column = "day",
  ylab = "Reported cases",
  Rt = NULL
)

plot_residuals(
  pred_dat,
  obs_dat,
  obj,
  value_column = "value",
  date_column = "day",
  type = c("raw", "quantile"),
  ylab = if (type == "raw") "Residual" else "Quantile residual",
  date_function = lubridate::ymd,
  return_residuals = FALSE
)

Arguments

pred_dat	Output from `tidy_seir()`.
obs_dat	A data frame of observed data. Should have a column of `day` and `value` that matches `pred_dat`. If using multiple data types, should also have `data_type`.
col	Colour for the line and ribbon.
value_column	Column in `obs_dat` that contains the reported cases.
date_column	Date or day column name. A column by this name must be in `obs_dat` and `pred_dat`. Note that `tidy_seir()` will return a data frame with `day` in it. If you want dates then you will need to add such a column.
ylab	Y axis label.
Rt	An optional vector of Rt values to colour the plot by.
obj	Outut from `fit_seir()`.
type	Raw (observed - expected) or quantile residuals (`covidseir:::qres_nbinom2`)?
date_function	A function to translate the character representation of
return_residuals	Return residuals instead of plot?

Value

A ggplot object

Details

See project_seir() for an example.

Examples

# See ?project_seir