Generation interval corresponding to the sample gostic_toy_rt dataset
gostic_gt_pmf.RdGostic et al., 2020 simulates data from a stochastic SEIR model. Residence
time in both the E and the I compartments is exponentially distributed, with
a mean of 4 days (or a rate/inverse-scale of 1/4). These residence times
imply a gamma-distributed generation time distribution with a shape of 2 and
a rate of 1/4. We convert the continuous gamma distribution into a PMF to use
with {RtGam}.
Details
From this parametric specification, we produce a double-censored,
left-truncated probability mass function of the generation interval
distribution. We produce the PMF using {epinowcast}'s
simulate_double_censored_pmf() with version 0.3.0. See
https://doi.org/10.1101/2024.01.12.24301247 for more information on
double-censoring biases and corrections.
We correct the output from simulate_double_censored_pmf() to make it
appropriate to use with {EpiNow2}. The function returns a numeric vector,
with the position of the element corresponding to one day more than the
length of the delay and value corresponding to the amount of discretized
probability density in the bin. The vector does not necessarily sum to one.
We drop the first element of the vector, which corresponds to a zero-day
delay. The renewal framework, which underpins our model does not account for
zero-day delays. We renormalize the left-truncated vector to sum to one so
that it's a proper PMF.