R0 (version 1.2-10)

est.GT: Find the best-fitting GT distribution for a series of serial interval

Description

Find the best-fitting GT distribution for a series of serial interval

Usage

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

Value

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

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 adjsument be displayed at the end?

...

Parameters passed to other functions (useful for hidden parameters of generation.time)

Author

Pierre-Yves Boelle, Thomas Obadia

Details

Generation Time 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 be of same length. Element i is the onset date for individual i. This means 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 record is assumed to be the time elapsed between each pair of infector and infectee.

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

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)