naomi-dev

Development version of model for joint small-area estimation of HIV prevalence, ART coverage, and HIV incidence, provisionally named Naomi.

Data

The relational diagramme below summarises the data elements required for model inputs.

The directory data-raw contains scripts for preparing data inputs from primary data sources. Following the relational model, data inputs are recommended to be prepared in the following order:

• data-raw/shapefile/: creates the location hierarchy and area boundaries.
• data-raw/population/: creates population by area, sex, and age group, and aggregated population (15-49, 15-64, 15+).
• data-raw/survey/: analyses household survey data for area-level survey estimates of prevalence, ART coverage, viral load suppression, and recent HIV infection.
• data-raw/programme/: creates datasets for for number receiving ART and routine antenatal HIV testing (ANC-RT).

District-level data for MPHIA 2015-16 are simulated for illustrative purposes by randomly allocating survey clusters within each stratum to districts proportionally to population size. See script data-raw/surveys/surveys.R for simulated district allocation.

The directory data contains processed data inputs:

• data/shapefile.rda: shapefile for area boundaries and hierarchy.
• data/population.rda: two datasets pop_agesex for population stratified by area, sex, and 5-year age-group, and pop_aggr with area-level aggregate population.
• data/survey.rda: survey estimates for HIV prevalence, ART coverage, VLS, and recent infection at all levels of location hierarchy and various age/sex stratifications.
• data/programme.rda: aggregated area-level data for ART and ANC-RT by quarter.

Prepare model inputs

Load packages

library(tidyverse)
library(here)
library(sf)
library(rstan)

Load functions

source(here("R/car.R"))
source(here("R/art-attendance.R"))

Load data

load(here("data/shapefile.rda"))
load(here("data/population.rda"))
load(here("data/survey.rda"))
load(here("data/programme.rda"))

Prepare model inputs