Supporting data for thesis titled "SARS-CoV-2 viral shedding and transmission during COVID-19 pandemic in Hong Kong"
This dataset was developed supporting analyses presented in Chapters 5–8 of the thesis. The dataset is organized into three sections. The first section, shedding_covid, contains the data dictionary for hospital and epidemiological records used in Chapters 5–7. These records include de-identified patient records but cannot be shared publicly due to ethical and confidentiality restrictions.
The second section, ct_rt_hk, includes the R scripts and simulated data used in Chapter 7. These data were generated using stochastic transmission models to study COVID-19 transmission in Hong Kong, including synthetic line lists, testing delay distributions, and viral load patterns. The third section, CtRt_simulation, provides the simulated data and R scripts used in Chapter 8, which expands on the models in Chapter 7 to evaluate different scenarios. Both ct_rt_hk and CtRt_simulation are (or will be) openly available on GitHub under an open-access license, with accompanying documentation to ensure transparency and reproducibility.