Epiverse-TRACE

All

70 repositories

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•6•1•Updated Mar 10, 2026Mar 10, 2026
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•1•2•0•0•Updated Mar 10, 2026Mar 10, 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•0•Updated Mar 10, 2026Mar 10, 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
•7•0•0•0•Updated Mar 10, 2026Mar 10, 2026
epimodelac-en
Public
Training materials for the epimodelac workshop
R
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Other
•6•1•0•0•Updated Mar 10, 2026Mar 10, 2026
EpiTKit-FR
Public
R
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Other
•5•0•0•0•Updated Mar 10, 2026Mar 10, 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
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Other
•3•0•0•0•Updated Mar 10, 2026Mar 10, 2026
epitkit
Public
R
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Other
•5•0•7•4•Updated Mar 10, 2026Mar 10, 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 Mar 10, 2026Mar 10, 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•74•6•Updated Mar 10, 2026Mar 10, 2026
EpiTKit-EN
Public
R
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Other
•5•0•1•0•Updated Mar 10, 2026Mar 10, 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•2•Updated Mar 10, 2026Mar 10, 2026
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
•3•2•44•7•Updated Mar 10, 2026Mar 10, 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•31•5•Updated Mar 10, 2026Mar 10, 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
•
Other
•6•0•0•1•Updated Mar 10, 2026Mar 10, 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•43•2•Updated Mar 10, 2026Mar 10, 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
•960•1•23•3•Updated Mar 10, 2026Mar 10, 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•10•5•1•Updated Mar 9, 2026Mar 9, 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
•13•37•57•4•Updated Mar 2, 2026Mar 2, 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
•3•9•26•1•Updated Mar 2, 2026Mar 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•0•Updated Mar 2, 2026Mar 2, 2026
epiparameterDB
Public
Database of epidemiological parameters
r epidemiology data-package
r epidemiology data-package r-package epiverse
R
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Creative Commons Zero v1.0 Universal
•1•2•0•2•Updated Mar 1, 2026Mar 1, 2026
safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
r-package
r-package
R
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Other
•0•1•1•5•Updated Feb 20, 2026Feb 20, 2026
sivirep
Public
Data Wrangling and Automated Reports from 'SIVIGILA' source
r public-health colombia
r public-health colombia r-package epidemiological-surveillance epiverse
R
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Other
•6•42•7•2•Updated Feb 4, 2026Feb 4, 2026
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package
r epidemiology r-package data-cleaning epiverse
R
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Other
•4•11•17•0•Updated Jan 29, 2026Jan 29, 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•3•0•Updated Jan 29, 2026Jan 29, 2026
climateR0
Public
R
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Other
•1•4•6•7•Updated Jan 8, 2026Jan 8, 2026
showcasedata
Public
R
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Other
•0•0•0•7•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 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
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