Epiverse-TRACE

All

61 repositories

safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
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Other
•0•0•3•2•Updated Mar 12, 2025Mar 12, 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•7•25•2•Updated Mar 12, 2025Mar 12, 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•7•13•2•Updated Mar 12, 2025Mar 12, 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•10•4•Updated Mar 12, 2025Mar 12, 2025
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•1•0•0•Updated Mar 12, 2025Mar 12, 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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•4•18•18•2•Updated Mar 12, 2025Mar 12, 2025
tutorials-late
Public
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Other
•1•2•36•0•Updated Mar 11, 2025Mar 11, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
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Other
•4•3•39•1•Updated Mar 11, 2025Mar 11, 2025
cleanepi
Public
R package to clean and standardize epidemiological data
r epidemiology r-package data-cleaning epiverse
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•3•9•14•5•Updated Mar 11, 2025Mar 11, 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•8•9•2•Updated Mar 11, 2025Mar 11, 2025
etstats
Public
r r-package organisation-tool
R
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Creative Commons Zero v1.0 Universal
•0•1•2•0•Updated Mar 11, 2025Mar 11, 2025
epitkit
Public
R
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•2•0•6•2•Updated Mar 11, 2025Mar 11, 2025
tutorials-middle
Public
R
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Other
•2•3•64•0•Updated Mar 11, 2025Mar 11, 2025
research-compendium
Public
reproducible-research rstats pre-alpha english-language research-compendium carpentries-workbench
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Other
•0•1•19•1•Updated Mar 11, 2025Mar 11, 2025
tutorials-early
Public
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•3•2•40•4•Updated Mar 11, 2025Mar 11, 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
•933•1•23•0•Updated Mar 11, 2025Mar 11, 2025
simulist
Public
An R package for simulating line lists
r epidemiology r-package outbreaks linelist epiverse
R
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Other
•1•9•9•0•Updated Mar 10, 2025Mar 10, 2025
translation-epitkit
Public
HTML
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Mar 10, 2025Mar 10, 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•4•28•1•Updated Mar 10, 2025Mar 10, 2025
.github
Public
infrastructure continuous-integration quality-assurance defaults github-organization community-health r-package-automation
1•1•5•0•Updated Mar 7, 2025Mar 7, 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•3•Updated Mar 5, 2025Mar 5, 2025
numberize
Public
Convert words to numbers in English, French and Spanish
r-package r-programming
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Other
•3•4•2•1•Updated Mar 4, 2025Mar 4, 2025
epiparameterDashboard
Public
Explore the database of epidemiological parameters provided by the {epiparameterDB} package
R
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•0•0•1•3•Updated Mar 1, 2025Mar 1, 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•3•Updated Mar 1, 2025Mar 1, 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
•4•13•12•3•Updated Feb 27, 2025Feb 27, 2025
tutorials-middle-es
Public
0•0•1•0•Updated Feb 27, 2025Feb 27, 2025
ColOpenData
Public
ColOpenData is a package that acquires and wrangles Colombian socioeconomic, geospatial and climate data
r maps climate data-package colombia r-package demographics
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Other
•1•11•3•1•Updated Feb 26, 2025Feb 26, 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
•4•43•4•2•Updated Feb 26, 2025Feb 26, 2025
howto
Public
R
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Creative Commons Attribution 4.0 International
•2•4•63•1•Updated Feb 26, 2025Feb 26, 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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•4•9•19•3•Updated Feb 26, 2025Feb 26, 2025