Open-source R packages for epidemiological analysis, surveillance, population estimation and reproducible reporting. Source code and documentation are linked below.
Polio surveillance
Bayesian Spatiotemporal Modelling of Relative AFP Reporting
Compares non-polio AFP reporting in each district with its past reporting and the national pattern to help identify drops.
Polio surveillance
Retrieve and Prepare GPEI POLIS Surveillance Data
Downloads and cleans WHO POLIS data for analysis, with checks for data problems and downloads that can resume after an interruption.
Measles immunity
Spatiotemporal Measles Population Immunity Profiling
Reconstructs and projects measles population immunity by birth cohort, area and month from routine coverage, campaigns and population estimates.
Malaria subnational tailoring
Utility Functions for Data Preparation and Analysis in Subnational Tailoring of Malaria Interventions (SNT)
Prepares data for malaria subnational tailoring: reads DHIS2 exports, matches administrative names, calculates reporting rates and extracts raster data.
Malaria subnational tailoring
Analytical Methods for Sub-National Tailoring Workflows
Analytical methods for subnational tailoring: incidence estimation, imputation of routine health data, campaign performance metrics and small-area statistical methods. A companion to sntutils.
Population modelling
Model Fine-Scale Age-Structured Population Data using Open-Source Data
Estimates population by single year of age on a 5 km grid, using household surveys, gridded population data and administrative boundaries.
Population modelling
Small Area Population Estimation by Demographics
Uses Bayesian models (INLA-SPDE) to break down small-area population totals by age, sex and other groups, with uncertainty estimates.
Polio surveillance
For Processing and Validating Various Types of Epidemiological Data
Import, cleaning and validation tools for Global Polio Eradication Initiative datasets, written for the WHO AFRO polio data team.
Reporting
House Figure Theme and PowerPoint Deck Builder for Routine Reports
A ggplot2 figure theme, colour palettes and helpers that assemble a PowerPoint deck from a template for routine reports.
Data preparation
A Tidy Solution for Epidemiological Data
Tools for importing, checking and cleaning routine epidemiological data.
GitHub Documentation Archived on CRAN
Polio surveillance
Key Functions to Analyze Global Polio Surveillance Data
Core functions used by US CDC to analyse global polio surveillance data.
Polio surveillance
Download and process POLIS data
Downloads, caches and processes POLIS data for US CDC polio analytics.
“Co-author” and “Contributor” mark packages that others maintain. A contributor has written code for the package but is not listed as an author in its metadata.
I co-lead AHADI’s Community Code Library for Subnational Tailoring of Malaria Interventions with Jaline Gerardin. It covers the analyses used in national malaria strategic plans, in English and French.
Open the SNT Code Library. The case study describes how it is used in country work.
Earlier packages from the WHO AFRO weekly surveillance reporting work, kept public on GitHub.