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Plot a proportions timeseries

Source: R/plot-prevalence-ts.R
plot_prevalence.Rd

Plot a proportions timeseries

Usage

plot_prevalence(
  modelled = i_prevalence_model,
  raw = i_proportion_data,
  ...,
  mapping = .check_for_aes(modelled, ...),
  events = i_events
)

Arguments

modelled

Proportion model estimates - a dataframe with columns:

  • time (ggoutbreak::time_period + group_unique) - A (usually complete) set of singular observations per unit time as a `time_period`

  • prevalence.0.025 (proportion) - lower confidence limit of prevalence (true scale)

  • prevalence.0.5 (proportion) - median estimate of prevalence (true scale)

  • prevalence.0.975 (proportion) - upper confidence limit of prevalence (true scale)

Any grouping allowed.

raw

Raw count data - a dataframe with columns:

  • denom (positive_integer) - Total test counts associated with the specified time frame

  • count (positive_integer) - Positive case counts associated with the specified time frame

  • time (ggoutbreak::time_period + group_unique) - A (usually complete) set of singular observations per unit time as a `time_period`

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.

mapping

a ggplot2::aes mapping. Most importantly setting the colour to something if there are multiple incidence timeseries 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 object

Examples

if(interactive()) {
  plot_prevalence(
    ggoutbreak::england_ons_infection_survey,
    mapping = ggplot2::aes(colour=geography))
}