github (overview)
github code repositories for malaria analytics in Uganda
ramptools (R package)
public
holds shared data assets (location table, indicator table, shapefiles) and functions for aggregating and accessing data
uga-etl-facility-data (repo)
private
Creates an initial database with facility reporting data from DHIS2, as well as code to update initial database. Bridges data from old and new instance of DHIS2. Creates “raw” and “clean” data. Clean data has undergone an outliering and imputation algorithm
uga-etl-spatial-hierarchy (repo) –
private
This repository has code for creating spatial files and spatial assets. This includes a master spatial file (pixelated grid), as well as shapefiles for subcounty, district, and region levels. This is also the repository for creating/updating the location table and facility tables that are stored in ramptools.
ramp.pop-catchment-estimates (repo)
private
Performs many pixel-level calculations to support estimations of catchment populations. This includes extracting population by pixel, locating nearest health facilities to each pixel based on walking and motorized travel times, then estimating catchment calculations based on populations that live around the facilities.
tpr_to_pfpr (repo)
private
The repository fits models to estimate PfPR from TPR, using MIS, DHS, and DHIS data. Then utilizes the models to predict TPR at the health facility or district level. Additional codes can estimate PfPR at the pixel level or other administrative levels. NOTE- this could be split into two repos- one with the exploration and one with the final model.
uga-survey-data (repo)
private
This repository contains code for pulling and formatting data from MIS, DHS and LLINEUP to allow for calculation of PfPR and merge with DHIS2 data. Frame/rename to be an ETL.
outbreak (repo)
Using time series data from the etl-facility-data, calculates outbreaks. Has code for calculating the outbreak index + code for generating shiny vis tool that displays the outputs.