Estimate the Generation Time Distribution for Days and Weeks
Source:R/get_generation_time_distribution.R
get_generation_time_distribution.RdThis function generates the generation time distribution for cholera from a
gamma distribution with shape mean_generation_time / 10 and a FIXED rate
of 0.1 per day, so only the shape responds to the mean (and the
coefficient of variation, \(1/\sqrt{shape}\), changes with it). The day-wise
and week-wise tables are saved as CSV files.
Arguments
- PATHS
A list containing the paths where the output tables will be saved. Typically generated by the
get_paths()function and should include:MODEL_INPUT: Path to the directory where model input data will be saved.
DOCS_TABLES: Path to the directory where day-wise and week-wise generation time tables will be saved.
- mean_generation_time
A numeric value representing the desired mean generation time (in days); sets the gamma shape (
mean_generation_time / 10) at a fixed rate of 0.1.
Details
The day-wise table (pred_generation_time_days.csv, column y) holds
the gamma density evaluated at days 1-56, not a probability mass
function: it is not normalised and omits the mass below day 1 and beyond day
56 (at a mean of 5 days it sums to about 0.74). Only the week-wise table
(Probability) is normalised to sum to 1. This is a legacy kernel: the
reproductive-number calculations (calc_Reff) derive their
generation-interval kernels from the model parameters and do not read these
files.