Epiverse-TRACE

All

66 repositories

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•10•19•4•Updated Jul 15, 2025Jul 15, 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 Jul 15, 2025Jul 15, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
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Other
•6•3•39•1•Updated Jul 15, 2025Jul 15, 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•13•2•Updated Jul 15, 2025Jul 15, 2025
superspreading
Public
Estimation of individual-level variation in transmission
r epidemiology r-package disease-transmission epiverse
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Other
•2•5•6•1•Updated Jul 15, 2025Jul 15, 2025
epiverse
Public
Meta-package for the Epiverse-TRACE R packages
r r-package epiverse
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Other
•0•1•1•1•Updated Jul 15, 2025Jul 15, 2025
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•2•0•0•Updated Jul 15, 2025Jul 15, 2025
etstats
Public
r r-package organisation-tool
R
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Creative Commons Zero v1.0 Universal
•0•1•2•1•Updated Jul 15, 2025Jul 15, 2025
epimodelac-en
Public
Training materials for the epimodelac workshop
R
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Other
•6•1•0•0•Updated Jul 15, 2025Jul 15, 2025
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
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Other
•6•8•18•3•Updated Jul 15, 2025Jul 15, 2025
epitkit
Public
R
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Other
•5•0•7•2•Updated Jul 15, 2025Jul 15, 2025
EpiTKit-EN
Public
R
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Other
•5•0•1•0•Updated Jul 15, 2025Jul 15, 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•37•1•Updated Jul 15, 2025Jul 15, 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 Jul 15, 2025Jul 15, 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
•6•3•38•5•Updated Jul 15, 2025Jul 15, 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 Jul 15, 2025Jul 15, 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 Jul 14, 2025Jul 14, 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 Jul 11, 2025Jul 11, 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•9•6•0•Updated Jul 7, 2025Jul 7, 2025
epiverselearner
Public
R
•0•0•0•0•Updated Jul 3, 2025Jul 3, 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•7•0•0•Updated Jun 27, 2025Jun 27, 2025
epiverse_demos
Public
R
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MIT License
•0•2•2•1•Updated Jun 27, 2025Jun 27, 2025
serofoi
Public
Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies
bayesian-methods epidemiology r-package antibodies serological-surveys stan-language epiverse r
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Other
•4•20•20•5•Updated Jun 26, 2025Jun 26, 2025
howto
Public
R
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Creative Commons Attribution 4.0 International
•2•4•69•4•Updated Jun 26, 2025Jun 26, 2025
.github
Public
infrastructure continuous-integration quality-assurance defaults github-organization community-health r-package-automation
MIT License
•2•1•3•0•Updated Jun 26, 2025Jun 26, 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•12•6•Updated Jun 26, 2025Jun 26, 2025
blueprints
Public
Software development blueprints for epiverse-trace
best-practices standards onboarding internal-docs standard-operating-procedure epiverse r-package-development
SCSS
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Other
•4•3•30•0•Updated Jun 24, 2025Jun 24, 2025
episoap
Public
[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
pipelines literate-programming epidemiology r-package decision-support automated-report rmarkdown-templates epiverse outbreak-analysis r
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•3•4•31•3•Updated Jun 24, 2025Jun 24, 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
•4•6•5•0•Updated Jun 24, 2025Jun 24, 2025