plot_projection: Plot a SEIR model projection

In seananderson/covidseir: Bayesian SEIR Modelling for Multivariate COVID-19 Case Data

Description

Plot a SEIR model projection

Usage

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?

Details

See project_seir() for an example.

Value

A ggplot object

Examples

# See ?project_seir

seananderson/covidseir documentation built on June 3, 2021, 6:49 a.m.