si {WhiteLabRt} | R Documentation |
Calculate a Serial Interval Distribution
Description
This function computes the probability distribution function (PDF) of the serial interval using a gamma distribution with specified shape and rate parameters. The serial interval is defined as the time between successive cases in a chain of transmission. This implementation generates a discrete PDF at the daily level.
Usage
si(ndays, shape, rate, leading0 = TRUE)
Arguments
ndays |
Integer, the number of days over which to calculate the serial interval distribution. |
shape |
Numeric, the shape parameter of the gamma distribution. |
rate |
Numeric, the rate parameter of the gamma distribution. |
leading0 |
Logical, should a leading 0 be added to indicate t0? |
Details
The function uses the pgamma
function to calculate cumulative
probabilities for each day up to ndays
and then differences these
to get daily probabilities. The resulting probabilities are normalized to
sum to 1, ensuring that they represent a valid probability distribution.
Value
Numeric vector representing the serial interval probabilities
for each of the first ndays
days. The probabilities are normalized
so that their sum is 1.
Examples
si(ndays = 14, shape = 4.29, rate = 1.18)