Reproduction number timeseries diagram

Usage

plot_rt(
  modelled = i_reproduction_number,
  ...,
  mapping = .check_for_aes(modelled, ...),
  events = i_events
)

Arguments

modelled

the modelled Rt estimate - a dataframe with columns:

time (ggoutbreak::time_period + group_unique) - A (usually complete) set of singular observations per unit time as a `time_period`
rt.fit (double) - an estimate of the reproduction number
rt.se.fit (positive_double) - the standard error of the reproduction number
rt.0.025 (double) - lower confidence limit of the reproduction number
rt.0.5 (double) - median estimate of the reproduction number
rt.0.975 (double) - upper confidence limit of the reproduction number

Any grouping allowed.

...

Named arguments passed on to geom_events

events

Significant events or time spans - a dataframe with columns:

label (character) - the event label
start (date) - the start date, or the date of the event
end (date) - the end date or NA if a single event

Any grouping allowed.

A default value is defined.

Named arguments passed on to geom_truth

true_df

a data frame with a time_period column called time and a value column (name given in true_col). This is optional and will be picked up from the raw parameter if given.

true_col

the column name / expression of the true value

true_fmt

a list of ggplot formatting to apply to the true value timeseries

...

Named arguments passed on to as.time_period

unit: the length of one unit of time. This will be either a integer number of days, or a specification such as "1 week", or another time_period. If x is a time_period, and the unit is different to that of x this will return a rescaled time_period using the new units.
start_date: the zero time date as something that can be coerced to a date. If the x input is already a time_period and this is different to its start_date then x will be recalibrated to use the new start date.
anchor: only relevant if x is a vector of dates, this is a date, or "start" or "end" or a weekday name e.g. "mon". With the vector of dates in x it will use this anchor to find a reference date for the time-series. If not provided then the current defaults will be used. (see set_defaults())

mapping

a ggplot2::aes mapping. Most importantly setting the colour to something if there are multiple incidence time series in the plot

events

Significant events or time spans - a dataframe with columns:

label (character) - the event label
start (date) - the start date, or the date of the event
end (date) - the end date or NA if a single event

Any grouping allowed.

A default value is defined.

Value

a ggplot timeseries

Examples

# example code
if (interactive()) {

tmp2 = example_poisson_locfit() %>%
  dplyr::filter(as.Date(time) >= "2021-01-01" & as.Date(time) < "2022-01-01") %>%
  rt_from_incidence(ip = example_ganyani_ip())

# comparing RT from growth rates with England consensus Rt
# (N.B. offset by 14 days to align with estimates):

plot_rt(tmp2,colour="blue")+
  ggplot2::geom_errorbar(
    data= ukc19::spim_consensus %>%
      dplyr::filter(date-14 >= "2021-01-01" & date-14 < "2022-01-01"),
    mapping=ggplot2::aes(x=date-14,ymin=rt.low,ymax=rt.high),
    colour="red")

}