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)
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.
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.