get_R: Estimate the Reproduction Number
In earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Description Usage Arguments Details Value Author(s) Examples

View source: R/get_R.R

This function estimates the (most of the time, 'basic') reproduction number (R) using i) the known distribution of the Serial Interval (delay between primary to secondary onset) and ii) incidence data.

get_R(x, ...)

## Default S3 method:
get_R(x, ...)

## S3 method for class 'integer'
get_R(
  x,
  disease = NULL,
  si = NULL,
  si_mean = NULL,
  si_sd = NULL,
  max_R = 10,
  days = 30,
  ...
)

## S3 method for class 'numeric'
get_R(x, ...)

## S3 method for class 'incidence'
get_R(x, ...)

`x`	The daily incidence to be used for inferring the reproduction number. Input can be an `incidence` object, as output by the package `incidence`, or a vector of numbers indicating daily number of cases. Note that 'zero' incidence should be reported as well (see details).
`...`	Further arguments to be passed to the methods.
`disease`	A character string indicating the name of the disease studied. If provided, then `si_mean` and `si_sd` will be filled in automatically using value from the literature. Accepted values are: "ebola".
`si`	A `distcrete` object (see package `distcrete`) containing the discretized distribution of the serial interval.
`si_mean`	The mean of the serial interval distribution. Ignored if `si` is provided.
`si_sd`	The standard deviation of the serial interval distribution. Ignored if `si` is provided.
`max_R`	The maximum value the reproduction number can take.
`days`	The number of days after the last incidence date for which the force of infection should be computed. This does not change the estimation of the reproduction number, but will affect projections.

The estimation of R relies on all available incidence data. As such, all zero incidence after the first case should be included in x. When using inidence from the 'incidence' package, make sure you use the argument last_date to indicate where the epicurve stops, otherwise the curve is stopped after the last case. Use as.data.frame to double-check that the epicurve includes the last 'zeros'.

A list with the earlyR class, containing the following components:

$incidence: the input incidence, in its original format
$R_grid: the grid of R values for which the likelihood has been computed.
$R_like: the values of likelihood corresponding to the $R_grid
$R_ml: the maximum likelihood estimate of R
$dates: the dates for which infectiousness has been computed
$lambdas: the corresponding values of force of infection
$si: the serial interval, stored as a distcrete object

Thibaut Jombart thibautjombart@gmail.com

if (require(incidence)) {

## example: onsets on days 1, 5, 6 and 12; estimation on day 24
 x <- incidence(c(1, 5, 6, 12), last_date = 24)
 x
 as.data.frame(x)
 plot(x)
 res <- get_R(x, disease = "ebola")
 res
 plot(res)

}