Growth rate timeseries diagram

Usage

plot_growth_rate(
  modelled,
  ...,
  mapping = .check_for_aes(modelled, ...),
  events = i_events
)

Arguments

modelled

a growth rate dataframe. - EITHER: a dataframe with columns:

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

Any grouping allowed.

OR with columns:

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

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

Examples


data = example_poisson_rt_2class()
tmp2 = data %>% poisson_locfit_model()

if(interactive()) {
  plot_growth_rate(tmp2)
}