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SI_simulation

Simulation Study for Estimating the Serial Interval: Appendix B

Title: Reliability Assessment of Outbreaker2 for Serial Interval Estimation

Abstract: This GitHub repository presents a simulation study conducted to evaluate the reliability of the outbreaker2 model in estimating the serial interval. The study utilises simulated data generated by the simulacr R package. The repository provides a reproducible example of the methods implemented in the serial_interval repository.

Instructions for Reproducing Results (Appendix B):

  1. Execute the following files:

    a. R/simulation_A.R: Compares the mean serial interval obtained from simulated data (simulacr) with the reconstructed serial interval (outbreaker2) using the true natural history moments.

    b. R/simulation_A.R: Compares the mean serial interval obtained from simulated data (simulacr) with the reconstructed serial interval (outbreaker2) under the mispecification of natural history parameters.

    c. R/simulation_A_B_plot.R: Generates a plot illustrating the results presented in Appendix B.

Please refer to the respective files for detailed code implementation.