Epiverse-TRACE

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70 repositories

etstats
Public
r r-package organisation-tool
JavaScript
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Creative Commons Zero v1.0 Universal
•1•1•0•0•Updated Jan 6, 2026Jan 6, 2026
epitkit
Public
R
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Other
•5•0•7•3•Updated Jan 6, 2026Jan 6, 2026
tutorials-middle
Public
Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated incidence data, superspreading from line list and contact data, and simulating transmission chains.
forecasting rstats english-language real-time-analysis outbreak-severity reproduction-number superspreading-events transmission-chain carpentries-workbench epiverse
R
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Other
•7•3•73•5•Updated Jan 6, 2026Jan 6, 2026
tutorials-early-fr
Public
Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.
R
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Other
•8•0•0•0•Updated Jan 6, 2026Jan 6, 2026
research-compendium
Public
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
R
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Other
•1•1•19•3•Updated Jan 6, 2026Jan 6, 2026
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
R
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Other
•6•8•18•3•Updated Jan 6, 2026Jan 6, 2026
epimodelac-en
Public
Training materials for the epimodelac workshop
R
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Other
•6•1•0•0•Updated Jan 6, 2026Jan 6, 2026
EpiTKit-FR
Public
R
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Other
•5•0•0•0•Updated Jan 6, 2026Jan 6, 2026
tutorials-late-fr
Public
Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.
R
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Other
•3•0•0•0•Updated Jan 6, 2026Jan 6, 2026
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
R
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Other
•8•3•43•1•Updated Jan 6, 2026Jan 6, 2026
tutorials-early
Public
Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.
data-validation exploratory-data-analysis data-visualization rstats data-cleaning english-language carpentries-workbench epiverse outbreak-analysis
R
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Other
•8•5•45•5•Updated Jan 6, 2026Jan 6, 2026
EpiTKit-EN
Public
R
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Other
•5•0•1•0•Updated Jan 6, 2026Jan 6, 2026
tutorials-late
Public
Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.
contact-matrix rstats vaccination contact-matrices burden-of-disease non-pharmaceutical-interventions carpentries-workbench epiverse outbreak-analysis infectious-disease-dynamics
R
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Other
•3•2•39•5•Updated Jan 6, 2026Jan 6, 2026
tutorials-middle-fr
Public
Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated incidence data, superspreading from line list and contact data, and simulating transmission chains.
R
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Other
•7•0•0•1•Updated Jan 6, 2026Jan 6, 2026
git-rstudio-basics
Public
Version Control with Git using Rstudio
github git version-control rstudio novice alpha-stage carpentries-workbench
R
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Other
•962•1•23•1•Updated Jan 6, 2026Jan 6, 2026
epiparameter
Public
R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases
r probability-distribution epidemiology data-package r-package data-access epiverse
R
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Other
•13•35•56•4•Updated Jan 5, 2026Jan 5, 2026
simulist
Public
An R package for simulating line lists
r epidemiology r-package outbreaks linelist epiverse
R
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Other
•1•10•6•1•Updated Jan 5, 2026Jan 5, 2026
epiparameterDB
Public
Database of epidemiological parameters
r epidemiology data-package r-package epiverse
R
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Creative Commons Zero v1.0 Universal
•1•2•0•0•Updated Jan 5, 2026Jan 5, 2026
superspreading
Public
Estimation of individual-level variation in transmission
r epidemiology r-package disease-transmission epiverse
R
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Other
•2•5•5•0•Updated Jan 5, 2026Jan 5, 2026
epichains
Public
Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models
epidemiology r-package r-stats epidemic-simulations branching-processes epidemic-modelling transmission-chain-reconstruction transmission-chain epidemiology-models outbreak-simulator
R
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Other
•3•8•26•1•Updated Jan 5, 2026Jan 5, 2026
showcasedata
Public
R
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Other
•0•0•0•7•Updated Jan 1, 2026Jan 1, 2026
safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
r-package
R
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Other
•0•1•1•5•Updated Jan 1, 2026Jan 1, 2026
finalsize
Public
R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility
r rcpp epidemiology r-package epidemic-modelling sdg-3 epiverse outbreak-analysis
R
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Other
•6•15•18•2•Updated Jan 1, 2026Jan 1, 2026
linelist
Public
R package for handling linelist data
data r data-structures epidemiology structured-data r-package outbreaks sdg-3 epiverse
R
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Other
•4•10•6•1•Updated Jan 1, 2026Jan 1, 2026
epiparameterDashboard
Public
Explore the database of epidemiological parameters provided by the {epiparameterDB} package
R
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Other
•0•0•1•4•Updated Jan 1, 2026Jan 1, 2026
vaccineff
Public
R package with tools for estimating vaccine effectiveness and vaccine related metrics
r epidemiology r-package epiverse vaccine-effectiveness
R
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Other
•4•16•4•2•Updated Jan 1, 2026Jan 1, 2026
climateR0
Public
R
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Other
•1•2•6•9•Updated Jan 1, 2026Jan 1, 2026
epidemics
Public
A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.
r rcpp epidemiology r-package decision-support vaccination scenario-analysis model-library epidemic-simulations rcppeigen
R
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Other
•5•15•18•8•Updated Jan 1, 2026Jan 1, 2026
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package data-cleaning epiverse
R
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Other
•4•10•17•1•Updated Jan 1, 2026Jan 1, 2026
cfr
Public
R package to estimate disease severity and under-reporting in real-time, accounting for reporting delays in epidemic time-series
r epidemiology r-package health-outcomes case-fatality-rate epidemic-modelling sdg-3 epiverse outbreak-analysis
R
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Other
•5•14•13•8•Updated Jan 1, 2026Jan 1, 2026