est.GT: Estimate generation time distribution

In tobadia/R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics

Estimate generation time distribution

Description

Find the best-fitting generation time distribution from a series of serial interval.

Usage

est.GT(
  infector.onset.dates = NULL,
  infectee.onset.dates = NULL,
  serial.interval = NULL,
  request.plot = FALSE,
  ...
)

Arguments

infector.onset.dates	Vector of dates for infector symptoms onset.
infectee.onset.dates	Vector of dates for infectee symptoms onset.
serial.interval	Vector of reported serial interval.
request.plot	Should data adjustment be displayed at the end?
...	Parameters passed to other functions (useful for hidden parameters of generation.time())

Details

Generation Time (GT) distribution can be estimated by two inputs methods. User can either provide two vectors of dates or a unique vector of reported serial intervals. If two vectors are provided, both ⁠*.onset.dates⁠ vectors should have the same length. The i-th element is the onset date for individual i. This implies that infector k (symptoms on day infector.onset.dates[k]) infected infectee k (symptoms on day infectee.onset.dates[k]). If only serial.interval is provided, each value is assumed to be the time elapsed between each pair of infector and infectee (i.e. the difference between the two ⁠*.onset.dates⁠ vectors).

When request.plot is set to TRUE, a graphical output provides standardized histogram of observed data along with the best-fitting adjusted model.

Value

A object of class R0.GT that complies with generation.time() distribution requirements of the R0 package.

Author(s)

Pierre-Yves Boelle, Thomas Obadia

Examples

#Loading package
library(R0)

# Data taken from traced cases of H1N1 viruses.
data(H1N1.serial.interval)
est.GT(serial.interval=H1N1.serial.interval)

## Best fitting GT distribution is a gamma distribution with mean = 3.039437 and sd = 1.676551 .
## Discretized Generation Time distribution
## mean: 3.070303 , sd: 1.676531 
## [1] 0.0000000000 0.1621208802 0.2704857362 0.2358751176 0.1561845680 0.0888997193 0.0459909903 
## 0.0222778094 0.0102848887 0.0045773285 0.0019791984 0.0008360608 0.0003464431 0.0001412594


# The same result can be achieved with two vectors of dates of onset.
# Here we use the same data, but trick the function into thinking onset dates are all "0".
data(H1N1.serial.interval)
est.GT(infector.onset.dates=rep(0,length(H1N1.serial.interval)), 
       infectee.onset.dates=H1N1.serial.interval)

tobadia/R0 documentation built on Sept. 24, 2023, 5:16 p.m.