SACEMA-UNITID Epidemiological Modelling Workshop

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Materials and Resources

Slides, code, and other materials are available below.

Case study 1: Dushoff et al. 2004

Introduction to Epidemiological Modelling

Paper discussion (wrap-up)

Code from live coding session

Coding Challenge 1

Summary of supplementary papers

Supplementary paper 1: Nyiro, Kombe, et al. 2017 Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya

Supplementary paper 2: Kucharski et al. 2015 Estimating the Life Course of Influenza A(H3N2) Antibody Responses from Cross-Sectional Data

Case study 2: Silkey et al. 2016

Topic 1: Models for study design

Paper discussion (wrap-up)

Code from coding session 2 (Download data sets: Cluster order, Household data)

Coding Challenge 2

Summary of supplementary papers

Supplementary paper 1: Cori et al. 2014 A Cluster-Randomized Trial of the Population Impact of an HIV Combination Prevention Intervention Including Universal Testing and Treatment: Mathematical Model

Supplementary paper 2: Bellan et al. 2015 Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis

Supplementary paper 3: Halloran et al. 2017 Simulations for designing and interpreting intervention trials in infectious diseases

Case study 3: WHO Rabies Modelling Consortium 2019

Topic 3: Structured model-based decision making

Paper discussion (wrap-up)

Code from coding session 3

Summary of supplementary papers

Supplementary paper 1: Li et al. 2017 Essential information: Uncertainty and optimal control of Ebola outbreaks

Supplementary paper 2: Probert et al. 2016 Decision-making for foot-and-mouth disease control: Objectives matter

Supplementary paper 3: Shea et al. 2014 Adaptive management and the value of information: learning via intervention in epidemiology

Supplementary paper 4: Probert et al. 2018 Real-time decision-making during emergency disease outbreaks

Example of using NetLogo to develop an individual-based model: Video, Code

Case study 4: Kucharski et al. 2015

Topic 4: Using models to infer impact of interventions

Paper discussion (wrap-up)

Summary of supplementary papers

Take-aways and follow-up

Supplementary paper 1: Silaba et al. 2019 Effect of 10-valent pneumococcal conjugate vaccine on the incidence of radiologically-confirmed pneumonia and clinically-defined pneumonia in Kenyan children: an interrupted time-series analysis

Supplementary paper 2: Bruhn et al. 2017 Estimating the population-level impact of vaccines using synthetic controls

Solutions for Coding Challenge 1

Solutions for Coding Challenge 2: Options 1 and 2, Option 3

Output for Coding Challenge 3: group live coding session

Sponsors

The workshop is made possible through an Africa Collaboration Grant from Stellenbosch University's International Office. Additional support is provided by the South African Center for Epidemioloigcal Modelling and Analysis (SACEMA, a DST-NRF Centre of Excellence), the University of Nairobi Institute for Tropical and Infectious Diseases (UNITID), Washington State University, the Infectious Disease Society of Kenya (IDSK), and the Kenya Education Network (KENET).

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