-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

 into agyw-tool-integration

…integration

Co-authored-by: Rob <[email protected]>

 into agyw-tool-integration

commit 551ada7
Author: Katie Risher <[email protected]>
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 <[email protected]>
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 <[email protected]>
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

Add KP adjustment for new infections

- 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

 into agyw-tool-integration