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    26 repositories

    • infection-dating-tool

      Public
      Django app for the Infection Dating Tool
      Python
      •
      GNU General Public License v3.0
      •1•0•0•3•Updated Apr 26, 2026Apr 26, 2026

    • inctools

      Public
      Incidence Estimation Tools
      cranstatisticsbiostatistics
      cranstatisticsbiostatisticsepidemiologyhivincidencebiomarkersinfectious-diseasesincidence-estimationincidence-inference
      GNU General Public License v3.0
      •4•6•8•0•Updated Nov 27, 2025Nov 27, 2025

    • reinfectionsBelinda

      Public
      Repository for Belinda's MSc work on reinfections
      R
      •
      Other
      •0•1•0•0•Updated Sep 19, 2023Sep 19, 2023

    • rd

      Public
      Research Days
      0•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • severity-monitoring

      Public
      SARS-CoV-2 severity monitoring project
      R
      •0•2•8•0•Updated Mar 17, 2023Mar 17, 2023

    • R_est_sa

      Public
      Code for the last steps in the reproduction number (R) estimation pipeline described in https://www.medrxiv.org/content/10.1101/2022.07.22.22277932v1.full
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 1, 2022Aug 1, 2022

    • omicronSA

      Public
      R
      •0•5•10•0•Updated Jun 23, 2022Jun 23, 2022

    • omicron_reinfections

      Public
      Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa (Pulliam et al. 2021)
      0•0•0•0•Updated Nov 30, 2021Nov 30, 2021

    • repo_template

      Public
      Repository template for student modelling projects
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 29, 2021Oct 29, 2021

    • secondWaves

      Public
      R
      •
      Other
      •0•0•0•0•Updated Feb 4, 2021Feb 4, 2021

    • SMART_testing

      Public
      Thinking about testing and interpretation of incidence data
      R
      •1•0•0•0•Updated Oct 28, 2020Oct 28, 2020

    • SACEMA.github.io

      Public
      SACEMA pages
      HTML
      •
      Other
      •0•0•0•0•Updated Jul 26, 2020Jul 26, 2020

    • COVID10k

      Public
      Estimating time to 10,000 COVID-19 cases in SA
      R
      •0•6•1•0•Updated Apr 6, 2020Apr 6, 2020

    • idd

      Public
      R Package for Infectious Disease Dynamics
      R
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Mar 24, 2020Mar 24, 2020

    • EpiEstim

      Public
      A tool to estimate time varying instantaneous reproduction number during epidemics
      R
      •40•0•0•0•Updated Mar 17, 2020Mar 17, 2020

    • DICE

      Public
      DICE: Dynamics of Interacting Community Epidemics
      R
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Aug 7, 2019Aug 7, 2019

    • listeriaOutbreak

      Public
      modeling decline of the listeriosis outbreak in SA
      R
      •
      Other
      •0•0•0•0•Updated Jul 30, 2019Jul 30, 2019

    • gitSandbox

      Public
      0•0•0•0•Updated Jul 15, 2019Jul 15, 2019

    • incidence-estimation.org

      Public
      The new website for incidence-estimation.org. Temporary URL:
      HTML
      •
      Other
      •17k•0•0•0•Updated Feb 22, 2019Feb 22, 2019

    • incidence-combined-method

      Public
      Analytical code for estimating incidence using a combination of demographic and biomarker-based approaches
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 17, 2018Sep 17, 2018

    • measlesOutbreak

      Public
      Measles outbreak in Stellenbosch
      0•0•0•0•Updated Feb 3, 2018Feb 3, 2018

    • openscience

      Public
      Repository for Open Science workshop at Research Days 2017
      1•0•0•0•Updated Aug 21, 2017Aug 21, 2017

    • pooled-pcr

      Public
      Cost-efficiency of pooled PCR testing for infant HIV diagnosis
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 25, 2017May 25, 2017

    • mdri-benchmarking

      Public
      Simulation code used for benchmarking MDRI estimation methods
      Python
      •1•0•0•0•Updated May 5, 2017May 5, 2017

    • R-course

      Public
      Repository for SACEMA's R programming short course
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 26, 2017Apr 26, 2017

    • incidence-synthetic-cohort

      Public
      Performs basic HIV incidence Estimation according to the method of Mahiane et al (A general HIV incidence inference scheme based on likelihood of individual lev…
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 1, 2015Sep 1, 2015
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