Epiverse-TRACE

All

63 repositories

epiCo
Public
R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia
r colombia r-package demographics decision-support spatio-temporal-analysis vector-borne-diseases sdg-3 epiverse outbreak-analysis
R
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Other
•2•12•7•3•Updated Jun 5, 2025Jun 5, 2025
git-rstudio-basics
Public
Version Control with Git using Rstudio
github git version-control rstudio novice alpha-stage carpentries-workbench
R
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Other
•945•1•23•0•Updated Jun 5, 2025Jun 5, 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
R
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Other
•1•2•37•1•Updated Jun 5, 2025Jun 5, 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
•5•3•38•2•Updated Jun 5, 2025Jun 5, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
R
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Other
•4•3•38•0•Updated Jun 5, 2025Jun 5, 2025
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•2•0•0•Updated Jun 5, 2025Jun 5, 2025
sivirep
Public
Data Wrangling and Automated Reports from 'SIVIGILA' source
public-health colombia r-package epidemiological-surveillance epiverse r
R
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Other
•5•42•4•2•Updated Jun 3, 2025Jun 3, 2025
translation-epitkit
Public
HTML
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Creative Commons Attribution 4.0 International
•0•0•0•1•Updated Jun 3, 2025Jun 3, 2025
etstats
Public
r r-package organisation-tool
R
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Creative Commons Zero v1.0 Universal
•0•1•0•0•Updated Jun 3, 2025Jun 3, 2025
epitkit
Public
R
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Other
•3•0•7•2•Updated Jun 3, 2025Jun 3, 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
R
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Other
•2•4•70•3•Updated Jun 3, 2025Jun 3, 2025
research-compendium
Public
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
R
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Other
•0•1•19•1•Updated Jun 3, 2025Jun 3, 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•2•8•3•Updated Jun 2, 2025Jun 2, 2025
.github
Public
infrastructure continuous-integration quality-assurance defaults github-organization community-health r-package-automation
MIT License
•2•1•3•0•Updated May 30, 2025May 30, 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
R
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Other
•13•36•54•2•Updated May 30, 2025May 30, 2025
epishowcase
Public
R
•0•0•3•0•Updated May 29, 2025May 29, 2025
linelist
Public
R package for handling linelist data
data r data-structures epidemiology structured-data r-package outbreaks sdg-3 epiverse
R
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Other
•4•8•7•2•Updated May 29, 2025May 29, 2025
packagetemplate
Public template
Template of an R package with standard Epiverse-TRACE automation
r r-package github-template template-repository
R
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Other
•4•6•6•2•Updated May 28, 2025May 28, 2025
epiverse
Public
Meta-package for the Epiverse-TRACE R packages
r r-package epiverse
R
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Other
•0•1•0•0•Updated May 28, 2025May 28, 2025
showcasedata
Public
R
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Other
•0•0•0•1•Updated May 28, 2025May 28, 2025
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package data-cleaning epiverse
R
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Other
•3•8•17•4•Updated May 27, 2025May 27, 2025
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-package epidemic-modelling sdg-3 epiverse outbreak-analysis
R
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Other
•7•12•16•1•Updated May 26, 2025May 26, 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
R
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Other
•2•6•27•2•Updated May 20, 2025May 20, 2025
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
R
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Other
•4•8•12•2•Updated May 13, 2025May 13, 2025
vaccineff
Public
R package with tools for estimating vaccine effectiveness and vaccine related metrics
epidemiology r-package epiverse vaccine-effectiveness r
R
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Other
•4•16•1•1•Updated May 12, 2025May 12, 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
R
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Other
•5•9•20•6•Updated May 8, 2025May 8, 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•11•1•Updated May 6, 2025May 6, 2025
climateR0
Public
R
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Other
•1•1•6•8•Updated May 6, 2025May 6, 2025
epiversetheme
Public
infrastructure r r-package organisation-tool community-health pkgdown-template epiverse
SCSS
•1•0•2•0•Updated Apr 28, 2025Apr 28, 2025
varnish
Public
Epiverse-TRACE fork of the Carpentries' workbench varnish package
SCSS
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Other
•39•0•0•2•Updated Apr 28, 2025Apr 28, 2025