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Plot the effective reproduction number

Source: R/sewer_plot.R
plot_R.Rd

Plots the effective reproduction number over time from one or several fitted EpiSewer models.

Usage

plot_R(
  results,
  draws = FALSE,
  ndraws = NULL,
  median = FALSE,
  seeding = FALSE,
  forecast = TRUE,
  forecast_horizon = NULL,
  date_margin_left = 0,
  date_margin_right = 0,
  facet_models = FALSE,
  facet_direction = "rows",
  base_model = "",
  model_levels = NULL,
  intervals = c(0.5, 0.95)
)

Arguments

results

Results object returned by EpiSewer() after model fitting. Can also be a named list with results from different model runs, in which case all results are plotted together and distinguished by colors.

draws

If FALSE (default), 50% and 95% Bayesian credible intervals are shown. If TRUE, exemplary posterior samples are shown in a "spaghetti plot" style.

ndraws

Number of different samples to show if draws=TRUE.

median

Should the estimated median be shown, or only the credible intervals? Default is FALSE to avoid over-interpretation of the median.

seeding

Should Rt from the seeding phase be shown as well? Default is FALSE.

forecast

Should forecasted Rt values be shown? Default is true. This requires that the model was fitted with a forecast horizon, see model_forecast().

forecast_horizon

How many days into the future should forecasts be plotted? Note that this is restricted by the forecast horizon specified during model fitting, see horizon_assume().

date_margin_left

By how many days into the past should the plot be expanded? Can also be negative to cut off some of the earliest dates.

date_margin_right

By how many days into the future should the plot be expanded? Can also be negative to cut off some of the latest dates.

facet_models

Should the plot be faceted by model? Default is FALSE.

facet_direction

How should the facetting be done? Either in different "rows" (default) or in different "columns".

base_model

Name of the base model (in the named list provided to results) which should be compared to the other models. This model will be plotted in black and will not be part of the legend.

model_levels

A character vector with the names of the models to be included. The colors and legend will be ordered according to the order in model_levels.

Value

A ggplot object showing the time series of estimated Rt, either with credible intervals or as "spaghetti plot". Can be further manipulated using ggplot2 functions to adjust themes and scales, and to add further geoms.