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70 repositories

tutorials-late
Public
Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling d…
contact-matrix rstats vaccination
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
•5•2•50•1•Updated Aug 21, 2026Aug 21, 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
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
•4•10•28•5•Updated Aug 20, 2026Aug 20, 2026
tutorials-middle
Public
Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated…
forecasting rstats english-language
forecasting rstats english-language real-time-analysis outbreak-severity reproduction-number superspreading-events transmission-chain carpentries-workbench epiverse
R
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Other
•6•3•79•2•Updated Aug 18, 2026Aug 18, 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
data-validation exploratory-data-analysis data-visualization rstats data-cleaning english-language carpentries-workbench epiverse outbreak-analysis
R
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Other
•7•5•32•1•Updated Aug 18, 2026Aug 18, 2026
epidemics
Public
A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes,…
r rcpp epidemiology
r rcpp epidemiology r-package decision-support vaccination scenario-analysis model-library epidemic-simulations rcppeigen
R
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Other
•6•19•12•3•Updated Aug 1, 2026Aug 1, 2026
vaccineff
Public
R package with tools for estimating vaccine effectiveness and vaccine related metrics
r epidemiology r-package
r epidemiology r-package epiverse vaccine-effectiveness
R
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Other
•5•17•5•3•Updated Jul 29, 2026Jul 29, 2026
tutorials
Public
rstats pre-alpha english-language
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
R
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Other
•7•3•48•3•Updated Jul 29, 2026Jul 29, 2026
howto
Public
Collection of reproducible how-to guides of Outbreak data analysis tasks using R packages.
howto exploratory-data-analysis real-time-analysis
howto exploratory-data-analysis real-time-analysis epiverse outbreak-analysis scenario-modeling
R
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Creative Commons Attribution 4.0 International
•2•4•76•4•Updated Jul 25, 2026Jul 25, 2026
epiverse-trace.github.io
Public
Technical blog of the Epiverse-TRACE project, where we share opinions and investigations in R package development, or scientific software development more gener…
blog epiverse quarto-website
blog epiverse quarto-website
R
•3•5•7•6•Updated Jul 2, 2026Jul 2, 2026
superspreading
Public
Estimation of individual-level variation in transmission
r epidemiology r-package
r epidemiology r-package disease-transmission epiverse
R
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Other
•2•5•5•3•Updated Jul 1, 2026Jul 1, 2026
etstats
Public
r r-package organisation-tool
r r-package organisation-tool
JavaScript
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Creative Commons Zero v1.0 Universal
•1•1•0•1•Updated Jul 1, 2026Jul 1, 2026
epiparameterDB
Public
Database of epidemiological parameters
r epidemiology data-package
r epidemiology data-package r-package epiverse
R
•
Creative Commons Zero v1.0 Universal
•1•3•0•3•Updated Jul 1, 2026Jul 1, 2026
simulist
Public
An R package for simulating line lists
r epidemiology r-package
r epidemiology r-package outbreaks linelist epiverse
R
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Other
•1•11•7•4•Updated Jul 1, 2026Jul 1, 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 dis…
r probability-distribution epidemiology
r probability-distribution epidemiology data-package r-package data-access epiverse
R
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Other
•14•38•56•5•Updated Jul 1, 2026Jul 1, 2026
personas
Public
R
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Creative Commons Attribution 4.0 International
•0•1•7•0•Updated Jun 25, 2026Jun 25, 2026
epiverselearner
Public
R
•1•0•0•0•Updated Jun 23, 2026Jun 23, 2026
readepi
Public
An R package for importing epi data into R.
r data-import epidemiology
r data-import epidemiology r-package epiverse health-information-systems
R
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Other
•5•6•4•1•Updated Jun 16, 2026Jun 16, 2026
varnish
Public
Epiverse-TRACE fork of the Carpentries' workbench varnish package
SCSS
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Other
•67•0•1•2•Updated Jun 12, 2026Jun 12, 2026
sandpaper
Public
[FORK] User Interface for The Carpentries Workbench
R
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Other
•33•0•0•1•Updated Jun 12, 2026Jun 12, 2026
linelist
Public
R package for handling linelist data
data r data-structures
data r data-structures epidemiology structured-data r-package outbreaks sdg-3 epiverse
R
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Other
•5•11•6•0•Updated Jun 6, 2026Jun 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
•
Other
•7•0•0•0•Updated May 12, 2026May 12, 2026
epimodelac-en
Public
Training materials for the epimodelac workshop
R
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Other
•6•1•1•0•Updated May 12, 2026May 12, 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 d…
R
•
Other
•5•0•0•0•Updated May 12, 2026May 12, 2026
epitkit
Public
R
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Other
•5•0•7•4•Updated May 12, 2026May 12, 2026
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
r rstats carpentries-workbench
R
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Other
•6•8•19•4•Updated May 12, 2026May 12, 2026
research-compendium
Public
reproducible-research rstats pre-alpha
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
R
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Other
•1•1•20•3•Updated May 12, 2026May 12, 2026
tutorials-middle-fr
Public
Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated…
R
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Other
•6•0•0•1•Updated May 12, 2026May 12, 2026
git-rstudio-basics
Public
Version Control with Git using Rstudio
github git version-control
github git version-control rstudio novice alpha-stage carpentries-workbench
R
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Other
•972•1•23•4•Updated May 12, 2026May 12, 2026
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•1•2•0•0•Updated Apr 24, 2026Apr 24, 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 rcpp epidemiology r-package epidemic-modelling sdg-3 epiverse outbreak-analysis
R
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Other
•6•15•22•0•Updated Mar 26, 2026Mar 26, 2026

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70 repositories