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

[biozj-tz]

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.

BDSIR_plot_1.0.1.R.txt

example.log

Best,

Jie

[denisekuehnert]

Dear Jie You can use the hpd package, see https://www.rdocumentation.org/packages/TeachingDemos/versions/2.13/topics/hpd Kind regards Denise El sáb, 20 sept 2025 a la(s) 12:22 p.m., biozj-tz ***@***.***) escribió:

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*biozj-tz* created an issue (BEAST2-Dev/phylodynamics#9) <#9> 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. BDSIR_plot_1.0.1.R.txt <https://github.com/user-attachments/files/22440051/BDSIR_plot_1.0.1.R.txt> example.log <https://github.com/user-attachments/files/22440056/example.log> Best, Jie — Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA6OQFJEUGCRCZEXLKWZQ3D3TUTGRAVCNFSM6AAAAACHBC2GTGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGQZTOMBQGQ3DINA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[biozj-tz]

Dear Jie

You can use the hpd package, see
https://www.rdocumentation.org/packages/TeachingDemos/versions/2.13/topics/hpd

Kind regards

Denise

El sáb, 20 sept 2025 a la(s) 12:22 p.m., biozj-tz @.***)
escribió:
…

Dear Denise,

Thanks your reply very much! You suggested use this hpd package, but would you mind show how to apply this to the log file from the BD-SIR model? Further, In fact, the boa library in R package can generate HPD of parameters, such as " boa.hpd" function, which was used to generate the HPD of reproductive numbers in the R script provided with the phylodynamics package. So can the HPDs of “ Prevalence ” and “ Incidence ” be generated by modifying the original R script?

Best,

Jie

[denisekuehnert]

Dear Jie Yes, you can just add it to the R script similar to how the median is computed. Either using boa.hpd or the other package. Best Denise El vie, 3 oct 2025 a la(s) 1:00 p.m., biozj-tz ***@***.***) escribió:

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*biozj-tz* left a comment (BEAST2-Dev/phylodynamics#9) <#9 (comment)> Dear Jie You can use the hpd package, see https://www.rdocumentation.org/packages/TeachingDemos/versions/2.13/topics/hpd Kind regards Denise El sáb, 20 sept 2025 a la(s) 12:22 p.m., biozj-tz *@*.***) escribió: … <#m_3350996895729093943_> Dear Denise, Thanks your reply very much! You suggested use this hpd package, but would you mind show how to apply this to the log file from the BD-SIR model? Further, In fact, the boa library in R package can generate HPD of parameters, such as " boa.hpd" function, which was used to generate the HPD of reproductive numbers in the R script provided with the phylodynamics package. So can the HPDs of “ Prevalence ” and “ Incidence ” be generated by modifying the original R script? Best, Jie — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA6OQFI5P2LDKRSFQ34OGYD3VZJLXAVCNFSM6AAAAACHBC2GTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGNRVGI3DENZTGA> . You are receiving this because you commented.Message ID: ***@***.***>