Epiverse-TRACE

All

67 repositories

etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•2•0•0•Updated Aug 26, 2025Aug 26, 2025
etstats
Public
r r-package organisation-tool
R
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Creative Commons Zero v1.0 Universal
•0•1•1•0•Updated Aug 26, 2025Aug 26, 2025
epimodelac-en
Public
Training materials for the epimodelac workshop
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Other
•6•1•0•0•Updated Aug 26, 2025Aug 26, 2025
EpiTKit-FR
Public
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Other
•5•0•0•0•Updated Aug 26, 2025Aug 26, 2025
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
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Other
•4•4•72•1•Updated Aug 26, 2025Aug 26, 2025
epitkit
Public
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Other
•5•0•7•1•Updated Aug 26, 2025Aug 26, 2025
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
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Other
•6•8•18•3•Updated Aug 26, 2025Aug 26, 2025
EpiTKit-EN
Public
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Other
•5•0•1•0•Updated Aug 26, 2025Aug 26, 2025
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
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Other
•2•2•36•2•Updated Aug 26, 2025Aug 26, 2025
research-compendium
Public
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
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Other
•1•1•19•2•Updated Aug 26, 2025Aug 26, 2025
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
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Other
•7•3•38•6•Updated Aug 26, 2025Aug 26, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
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Other
•7•3•40•0•Updated Aug 26, 2025Aug 26, 2025
git-rstudio-basics
Public
Version Control with Git using Rstudio
github git version-control rstudio novice alpha-stage carpentries-workbench
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Other
•949•1•23•1•Updated Aug 26, 2025Aug 26, 2025
readepi
Public
An R package for importing epi data into R.
r data-import epidemiology r-package epiverse health-information-systems
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Other
•5•6•12•1•Updated Aug 25, 2025Aug 25, 2025
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 generally
blog epiverse quarto-website
R
•3•3•6•2•Updated Aug 25, 2025Aug 25, 2025
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•1•Updated Aug 22, 2025Aug 22, 2025
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
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Other
•13•35•56•6•Updated Aug 22, 2025Aug 22, 2025
superspreading
Public
Estimation of individual-level variation in transmission
r epidemiology r-package disease-transmission epiverse
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Other
•2•5•5•0•Updated Aug 22, 2025Aug 22, 2025
simulist
Public
An R package for simulating line lists
r epidemiology r-package outbreaks linelist epiverse
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Other
•1•10•5•2•Updated Aug 21, 2025Aug 21, 2025
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package data-cleaning epiverse
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Other
•3•8•19•3•Updated Aug 19, 2025Aug 19, 2025
epiverse
Public
Meta-package for the Epiverse-TRACE R packages
r r-package epiverse
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Other
•0•1•0•2•Updated Aug 19, 2025Aug 19, 2025
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
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Other
•3•6•27•5•Updated Aug 19, 2025Aug 19, 2025
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
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Other
•5•15•13•7•Updated Aug 15, 2025Aug 15, 2025
translation-epitkit
Public
R
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Creative Commons Attribution 4.0 International
•0•2•0•0•Updated Aug 8, 2025Aug 8, 2025
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
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Other
•5•11•17•7•Updated Aug 6, 2025Aug 6, 2025
howto
Public
R
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Creative Commons Attribution 4.0 International
•2•4•66•4•Updated Jul 31, 2025Jul 31, 2025
packagetemplate
Public template
Template of an R package with standard Epiverse-TRACE automation
r r-package github-template template-repository
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Other
•5•6•5•1•Updated Jul 19, 2025Jul 19, 2025
safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
r-package
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Other
•0•1•1•0•Updated Jul 8, 2025Jul 8, 2025
linelist
Public
R package for handling linelist data
data r data-structures epidemiology structured-data r-package outbreaks sdg-3 epiverse
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Other
•4•10•6•0•Updated Jul 7, 2025Jul 7, 2025
epiverselearner
Public
R
•0•0•0•0•Updated Jul 3, 2025Jul 3, 2025