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, <b>s</b><b>hedding_</b><b>covid</b>, 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, <b>c</b><b>t</b><b>_r</b><b>t_</b><b>hk</b>, 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, <b>CtRt_</b><b>s</b><b>imulation</b>, 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.