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Generation interval corresponding to the sample stochastic_sir_rt dataset

Source: R/data.R
sir_gt_pmf.Rd

Gostic 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. The distribution can be regenerated in data-raw/sir_gt_pmf.R.

Usage

sir_gt_pmf

Format

sir_gt_pmf A numeric vector of length 26 that sums to one within numerical tolerance

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 primarycensored::dpcens() with version 0.4.0. See https://doi.org/10.1101/2024.01.12.24301247 for more information on double-censoring biases and corrections.

References

Gostic, Katelyn M., et al. "Practical considerations for measuring the effective reproductive number, Rt." PLoS computational biology 16.12 (2020): e1008409.