These functions are designed for plotting earlyR objects, output by
the function get_R. It can plot either the likelihood of R
values, or the force of infection over time (see argument type). For
points, the latter is used.
# S3 method for earlyR plot(x, type = c("R", "lambdas"), scale = "ml", ...) # S3 method for earlyR points(x, scale = 1, ...)
| x | A |
|---|---|
| type | The type of graphic to be generated, matching either "R" or "lamdbas"; "R" will plot the likelihood of R values; "lambdas" will plot the force of infection over time; see `scale` argument to interprete the force of infection. |
| scale | A numeric value indicating the total number of new cases expected over the time period of the lambdas, or a recognised `character` string; lambdas will be scaled to correspond to the number of expected cases every day; defaults to `ml`, which tells function to use the maximum likelihood estimate of *R* multiplied by the number of infectious cases |
| ... | Further arguments to be passed to other methods; for the plot of *R*, `...` is passed to `ggplot2::geom_line()`; for the plot of *lambdas*, `...` is passed to `ggplot2::geom_bar()`. |
A `ggplot2` object.
if (require(incidence)) ## example: onsets on days 1, 5, 6 and 12; estimation on day 24 onset <- c(1, 5, 6, 12) x <- incidence(onset, last_date = 24) xres <- get_R(x, disease = "ebola") res plot(res) plot(res, "lambdas")
Thibaut Jombart thibautjombart@gmail.com