SHIPP tool update incidence #428
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-Adds comments & sources -Corrects minor issues w/translation of code -Updates KP calculations based on updated data -Corrects age distribution of MSM to reflect age at sexual debut by country
commit 551ada7 Author: Katie Risher <krisher@ic.ac.uk> Date: Fri Jan 19 16:53:00 2024 -0500 Additional edits to the agyw integration functions -New infections instead of incidence for the Naomi outputs tab -Naming the countries to match the tool -some edits so the area names are formatted more nicely -max RR for FSW capped at 35 - if over 35 leads to impossible incidence estimates in some districts commit 666c504 Author: Katie Risher <krisher@ic.ac.uk> Date: Sun Dec 17 22:08:52 2023 -0500 Add outputs argument to agyw_calculate_prevalence_male Add outputs argument to agyw_calculate_prevalence_male commit 0d35296 Author: Katie Risher <krisher@ic.ac.uk> Date: Thu Dec 14 23:05:36 2023 -0500 Remove rr_sexnonreg Remove rr_sexnonreg from female output
add placeholder for incidence adjustment code
Added KP adjustment to incidence estimates to match Spectrum KP new infection estimates for women & men - results in updated estimates of incidence for other behavioural groups as well
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Initiated a PR to update branch pse-tool-update-incidence here: #430 (Note: I don't have permission to make any changes on mrc-ide/naomi, hence all the PRs from my fork) |
- Align SHIPP vignette with the methods used - Minor code fixes for adjusting KP new infections to either KP workbook or Goals estimates under the assumption that a consensus KP new infection estimate is never missing
…e/naomi into pse-tool-update-incidence
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Closed and pulled into: #413 |
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Currently: Incidence rates are distributed between those with single cohabiting partner, those with non-regular partner(s), and KPs using a uniform IRR for non-regular vs cohabiting, and an IRR based on incidence/prevalence for KPs vs cohabiting.
Updated methods: reweighting the district-specific IRRs based on both KP size + incidence in the district to the national # new infections for KPs.