Skip to content

Xin hpv infection process #1860

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
tdm32 wants to merge 10 commits into
base: master
Choose a base branch
from
Draft

Xin hpv infection process #1860

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
6af9c18
This is the first draft of HPV model
Liuxinac Mar 2, 2026
8a7bb49
Add 3 HPV groups, simple sexual mixing, and self-clearance
Liuxinac Mar 25, 2026
8d221b9
add group-specific HPV self-clearance timing and annual logging
Liuxinac Apr 1, 2026
bb183fc
Update HPV module: add natural immunity, HIV/age/vaccination modifier…
Liuxinac Apr 14, 2026
b535f42
Add HPV resource files
Liuxinac Apr 14, 2026
3ccf652
Update HPV module: add natural immunity, HIV/age/vaccination modifier…
Liuxinac Apr 15, 2026
42bfc28
Update HPV self-clearance process
Liuxinac Apr 15, 2026
68dbf74
Refine HPV self-clearance logic
Liuxinac Apr 27, 2026
f465f10
HPV Transmission Model Version 1.0
Liuxinac Apr 30, 2026
4e540d6
HPV Transmission Model Version 1.0
Liuxinac May 5, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion resources/ResourceFile_Cervical_Cancer/parameter_values.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,4 +52,4 @@ months_to_next_appt_treated_less_than_12_mo_ago,3,local,1,36,vague prior,Missing
months_to_next_appt_treated_12_to_36_mo_ago,6,local,1,36,vague prior,Missing
months_to_next_appt_treated_36_to_60_mo_ago,12,local,1,36,vague prior,Missing
palliative_care_interval_months,1,local,0.5,12,vague prior,Missing
main_polling_frequency_months,1,undetermined,1,12,design decision,N/A
main_polling_frequency_months,1,undetermined,1,12,design decision,N/A
17 changes: 17 additions & 0 deletions resources/ResourceFile_HPV/parameter_values.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
parameter_name,value,param_label,prior_min,prior_max,prior_note,reference,
init_prev_hpv_hr1,0.05,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. ",
init_prev_hpv_hr2,0.1,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. ",
init_prev_hpv_hr3,0.06,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. ",
b_hpv,0.3,undetermined,0,1,calibration,N/A,
rr_hpv_hiv_no_art,2.6,undetermined,0,1,calibration,"Liu G, Sharma M, Tan N, Barnabas RV. HIV-positive women have higher risk of human papilloma virus infection, precancerous lesions, and cervical cancer. AIDS. 2018 Mar 27;32(6):795-808. doi: 10.1097/QAD.0000000000001765. PMID: 29369827; PMCID: PMC5854529.",
rr_hpv_hiv_art_unsuppressed,1.8,undetermined,0,1,calibration,N/A,
rr_hr1_vaccinated,0.1,undetermined,0,1,calibration,N/A,
rr_hr2_vaccinated,0.5,undetermined,0,1,calibration,N/A,
rr_hr3_vaccinated,0.8,undetermined,0,1,calibration,N/A,
rr_hpv_age50plus,0.5,undetermined,0,1,calibration,N/A,
median_clear_hr1,14,undetermined,0,1,calibration,N/A,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr2,12,undetermined,0,1,calibration,N/A,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr3,12,undetermined,0,1,calibration,N/A,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
clear_shape,1,undetermined,0,1,calibration,N/A,
rr_clear_hiv_no_art,0.65,undetermined,0,1,calibration,N/A,
rr_clear_hiv_art_unsuppressed,0.8,undetermined,0,1,calibration,N/A,
Loading
Loading