Software & Teaching

Below is a summary of my open source contributions. Find my GitHub page here.

I also review open-source R code and packages for journals like the Journal of Open Source Software.

Do reach out if you need my services.

Open-Source Software

I lead and contribute to several open-source communities developing R packages for outbreak analytics. You can explore all my code on GitHub.

Epiverse TRACE

During my time as a Research Software Engineer with the Epiverse-TRACE Initiative, I:

  • Developed epichains as a successor of bpmodels for analyzing the distribution of the size and length of transmission chains

  • Co-maintained EpiNow2 for estimating the time-varying reproduction number, growth rate, and doubling time using Bayesian methods

epiforecasts community

I contribute to:

  • EpiNow2: Estimates the time-varying reproduction number, growth rate, and doubling time using a range of open-source tools and Bayesian methods

  • scoringutils: Tools for scoring and assessing predictions

epinowcast community

I contribute to:

  • epinowcast: Provides flexible and efficient methods for gaining situational awareness during outbreaks using currently available epidemiological observations and the reporting patterns of historical observations

The Carpentries

I briefly co-maintained the Carpentries course on Data Analysis and Visualization in R for Ecologists

Teaching & Outreach

Current Teaching

I am the lead facilitator for the Modelling for Pandemic Preparedness and Response (MPPR) modular shortcourse hosted by The German-West African Centre for Global Health and Pandemic Prevention (G-WAC) at the College of Health Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.

Course Objectives/Learning Outcomes:

At the end of the course, participants are expected to:

  • Understand the concepts of infectious disease transmission and control
  • Enhance knowledge about data sources, data access, and data curation in (West) Africa
  • Design, implement and use context-specific mathematical models using the R programming language
  • Improve knowledge of communication about modeling output
  • Become part of a network of disease modelers with an interest in West Africa

We have successfully delivered two iterations of this course in 2024 and 2025.

I also maintain a YouTube channel with over 3,500 subscribers, featuring tutorials like this Mendeley tutorial with over 36,000 views.

Teaching Competencies

  • Mathematical/statistical/dynamical modeling of infectious diseases
    • Introduction to Compartmental Models including methods for estimating the basic reproduction number. See example materials.
    • Model fitting techniques. See example materials.
    • Basics of branching process models for infectious disease modelling
    • Introduction to Bayesian Models for Infectious Disease Forecasting
    • Developing generative Bayesian models for forecasting infectious diseases
    • Forecast evaluation using metrics such as Proper Scoring Rules
  • Reproducible data analysis workflows
    • R programming from the basics to advanced topics (package development, object-oriented programming)
    • Research software/code development best practices
    • Git/GitHub from the basics to intermediate/advanced (merging and rebasing, cherry-picking, etc.)
    • R package development using software engineering industry standards
    • Pipeline orchestration with GNU make and the targets R package
    • Reproducible environments and research code portability (docker, renv, etc)
  • Evidence synthesis
    • Systematic/scoping review methods and free automation tools like Rayyan. See my YouTube tutorials
  • Thesis and journal article writing techniques

Previous Teaching Experience

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