Epiverse-TRACE

All

68 repositories

etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•2•1•0•Updated Sep 19, 2025Sep 19, 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•2•1•Updated Sep 17, 2025Sep 17, 2025
sivirep
Public
Data Wrangling and Automated Reports from 'SIVIGILA' source
public-health colombia r-package epidemiological-surveillance epiverse r
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Other
•6•42•5•2•Updated Sep 16, 2025Sep 16, 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•74•2•Updated Sep 16, 2025Sep 16, 2025
etstats
Public
r r-package organisation-tool
JavaScript
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Creative Commons Zero v1.0 Universal
•1•1•0•0•Updated Sep 16, 2025Sep 16, 2025
tutorials-early-fr
Public
Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.
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Other
•9•0•0•0•Updated Sep 16, 2025Sep 16, 2025
epimodelac-en
Public
Training materials for the epimodelac workshop
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Other
•6•1•0•0•Updated Sep 16, 2025Sep 16, 2025
EpiTKit-FR
Public
R
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Other
•5•0•0•0•Updated Sep 16, 2025Sep 16, 2025
epitkit
Public
R
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Other
•5•0•7•3•Updated Sep 16, 2025Sep 16, 2025
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
R
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Other
•6•8•18•3•Updated Sep 16, 2025Sep 16, 2025
EpiTKit-EN
Public
R
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Other
•5•0•1•0•Updated Sep 16, 2025Sep 16, 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•3•Updated Sep 16, 2025Sep 16, 2025
research-compendium
Public
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
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Other
•1•1•19•3•Updated Sep 16, 2025Sep 16, 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
R
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Other
•9•4•44•5•Updated Sep 16, 2025Sep 16, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
R
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Other
•7•3•42•1•Updated Sep 16, 2025Sep 16, 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
•953•1•23•1•Updated Sep 16, 2025Sep 16, 2025
epiverse
Public
Meta-package for the Epiverse-TRACE R packages
r r-package epiverse
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Other
•0•1•0•1•Updated Sep 11, 2025Sep 11, 2025
translation-epitkit
Public
R
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Creative Commons Attribution 4.0 International
•0•2•0•0•Updated Sep 10, 2025Sep 10, 2025
epi-training-kit
Public template
An e-learning strategy for training on analysis, modelling and response to outbreaks and epidemics in Latin-America and the Caribbean
training data-science e-learning epidemics
R
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Creative Commons Attribution 4.0 International
•1•10•0•0•Updated Sep 10, 2025Sep 10, 2025
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package data-cleaning epiverse
R
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Other
•4•9•18•0•Updated Sep 10, 2025Sep 10, 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•1•Updated Sep 3, 2025Sep 3, 2025
showcasedata
Public
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Other
•0•0•0•2•Updated Sep 2, 2025Sep 2, 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•3•Updated Sep 2, 2025Sep 2, 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 Sep 1, 2025Sep 1, 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•7•26•3•Updated Aug 29, 2025Aug 29, 2025
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 Aug 28, 2025Aug 28, 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•4•Updated Aug 27, 2025Aug 27, 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
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
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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•5•11•17•7•Updated Aug 6, 2025Aug 6, 2025