How to obtain the upper and lower limits of the 95% HPD of the two parameters of “ Prevalence ” and “ Incidence ” in Birth Death-SIR model

[Jie Zha]

Hi,

About the two parameters of “ Prevalence  ” and “ Incidence ” estimated by the Birth Death-SIR model in BEAST 2,  we can only obtain the median values of these two parameters through the R script provided with the phylodynamics package. But if I want to obtain the upper and lower limits of their 95% HPD. How should I modify the script to effect this purpose ?

I attached the script and my example dataset for you to check.

https://github.com/user-attachments/files/22440051/BDSIR_plot_1.0.1.R.txt
https://github.com/user-attachments/files/22440056/example.log

Best,

Jie