multi-agyw

Code for the paper Howes et al. "Spatio-temporal estimates of HIV risk group proportions for adolescent girls and young women across 13 priority countries in sub-Saharan Africa" (PLOS Global Public Health)

Note

This work has now been extended to include males, as well as additional countries. See the UNAIDS Sub-national HIV Estimates in Priority Populations (SHIPP) tool.

Summary

New HIV infections are disproportionately common in adolescent girls and young women (AGYW). Accelerating provision of HIV prevention programming for AGYW is a top priority, but funding is insufficient to reach everyone (HIV Prevention Coalition, 2020). Small-area estimation of risk group population sizes enables countries to prioritise provision of services to those at greatest risk, taking into account both geographic and behavioral factors, as called for in the Global AIDS Strategy 2021-2026. Using AIS, BAIS, DHS and PHIA survey data, we fit multinomial logistic regressions to priority countries using the package R-INLA. To enable inference with the R-INLA package, each model is reformulated as an equivalent Poisson log linear model using the multinomial-Poisson transformation (Baker, 1994). We use the resulting proportion estimates to disaggregate HIV prevalence and HIV incidence estimates from the Naomi small-area estimation model according to risk group membership.

Citation

If you would like to cite this work, please use:

@article{howes2023spatio,
    doi = {10.1371/journal.pgph.0001731},
    author = {Howes, Adam and Risher, Kathryn A. and Nguyen, Van Kính and Stevens, Oliver and Jia, Katherine M. and Wolock, Timothy M. and Esra, Rachel T. and Zembe, Lycias and Wanyeki, Ian and Mahy, Mary and Benedikt, Clemens and Flaxman, Seth R. and Eaton, Jeffrey W.},
    journal = {PLOS Global Public Health},
    publisher = {Public Library of Science},
    title = {{Spatio-temporal estimates of HIV risk group proportions for adolescent girls and young women across 13 priority countries in sub-Saharan Africa}},
    year = {2023},
    month = {04},
    volume = {3},
    url = {https://doi.org/10.1371/journal.pgph.0001731},
    pages = {1-14},
    number = {4}
}

File structure

The directories of this repository are:

Directory	Contains
make	Scripts used to run the reports. _make.R runs everything in order.
misc	Miscellaneous code, not used as part of orderly.
src	All orderly reports.
tutorials	Miscellaneous code used to study models and get up to speed.
utils	Helper scripts for common development tasks.

orderly

We use the orderly package (RESIDE, 2020) to simplify the process of doing reproducible research. After installing orderly (from either CRAN or Github) a report, example, may be run by:

orderly::orderly_run(name = "src/example")

The results of this run will appear in the draft/ folder (ignored on Github). To commit the draft (with associated id) to the archive/ folder (also ignored on Github, and treated as "read only") use:

orderly::orderly_commit(id)

Any outputs of this report will then be available to use as dependencies within other reports. Reports can be pushed to the HIV inference group sharepoint (the remote) using:

orderly::orderly_push_archive("example")

Or can be pulled (alongside any dependencies) from the remote using:

orderly_pull_archive("example")

Alternatively, just the dependencies can be pulled using orderly::orderly_pull_dependencies("example").

R package dependencies

This repository is supported by the mutli.utils package, which can be installed from Github via:

devtools::install_github("athowes/multi.utils")

The R-INLA package is not currently available on CRAN, and instead may be installed by following instructions from the project website. This repository also requires a particular branch of the naomi.utils package, which can be installed from Github via:

devtools::install_github("athowes/naomi.utils", ref = "sexbehav-vars-adam")

Session information

The sessionInfo() used to run this analysis is:

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] multi.utils_0.1.0 stringr_1.5.0     purrr_1.0.1       readr_2.1.3      
 [5] tidyr_1.2.1       tibble_3.1.8      tidyverse_1.3.1   forcats_0.5.2    
 [9] ggplot2_3.4.0     dplyr_1.0.10      rmarkdown_2.18