Allows users to plot the output from
estimate_infections
easily. In future releases it
may be depreciated in favour of increasing the functionality of the S3 plot methods.
plot_estimates(
estimate,
reported,
ylab = "Cases",
hline,
obs_as_col = TRUE,
max_plot = 10,
estimate_type = NULL
)
A data.table of estimates containing the following variables: date, type (must contain "estimate", "estimate based on partial data" and optionally "forecast"),
A data.table of reported cases with the following variables: date, confirm.
Character string, defaulting to "Cases". Title for the plot y axis.
Numeric, if supplied gives the horizontal intercept for a indicator line.
Logical, defaults to TRUE
. Should observed data, if supplied, be plotted using columns or
as points (linked using a line).
Numeric, defaults to 10. A multiplicative upper bound on the number of cases shown on the plot. Based on the maximum number of reported cases.
Character vector indicating the type of data to plot. Default to all types with supported options being: "Estimate", "Estimate based on partial data", and "Forecast".
A ggplot2
object
# \donttest{
# define example cases
cases <- example_confirmed[1:40]
# set up example delays
generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
reporting_delay <- estimate_delay(rlnorm(100, log(6), 1), max_value = 10)
# run model
out <- estimate_infections(cases,
generation_time = generation_time,
delays = delay_opts(incubation_period, reporting_delay)
)
# plot infections
plot_estimates(
estimate = out$summarised[variable == "infections"],
reported = cases,
ylab = "Cases", max_plot = 2
) + ggplot2::facet_wrap(~type, scales = "free_y")
# plot reported cases estimated via Rt
plot_estimates(
estimate = out$summarised[variable == "reported_cases"],
reported = cases,
ylab = "Cases"
)
# plot Rt estimates
plot_estimates(
estimate = out$summarised[variable == "R"],
ylab = "Effective Reproduction No.",
hline = 1
)
#' # plot Rt estimates without forecasts
plot_estimates(
estimate = out$summarised[variable == "R"],
ylab = "Effective Reproduction No.",
hline = 1, estimate_type = "Estimate"
)
# }