Description Usage Arguments Details Value Author(s) Examples
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.
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x 
The daily incidence to be used for inferring the reproduction
number. Input can be an 
... 
Further arguments to be passed to the methods. 
disease 
A character string indicating the name of the disease
studied. If provided, then 
si 
A 
si_mean 
The mean of the serial interval distribution. Ignored if

si_sd 
The standard deviation of the serial interval
distribution. Ignored if 
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 doublecheck 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
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