Epiverse-TRACE

All

60 repositories

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
HTML
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Creative Commons Attribution 4.0 International
•1•7•0•0•Updated Feb 14, 2025Feb 14, 2025
epiverse_demos
Public
R
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MIT License
•0•0•0•1•Updated Feb 14, 2025Feb 14, 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
R
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Other
•4•18•15•2•Updated Feb 13, 2025Feb 13, 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
R
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Other
•1•11•3•0•Updated Feb 13, 2025Feb 13, 2025
sandpaper
Public
[FORK] User Interface for The Carpentries Workbench
R
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Other
•30•0•0•1•Updated Feb 13, 2025Feb 13, 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•11•16•1•Updated Feb 13, 2025Feb 13, 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
•4•8•19•2•Updated Feb 13, 2025Feb 13, 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•10•1•Updated Feb 12, 2025Feb 12, 2025
safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
R
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Other
•0•0•6•2•Updated Feb 12, 2025Feb 12, 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•0•Updated Feb 12, 2025Feb 12, 2025
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•1•1•0•Updated Feb 12, 2025Feb 12, 2025
Severity_methods_assessment
Public
Assessment of severity estimation methods during an infectious disease outbreak
R
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GNU General Public License v2.0
•0•0•0•1•Updated Feb 11, 2025Feb 11, 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
R
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Other
•4•13•11•1•Updated Feb 11, 2025Feb 11, 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
R
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Other
•2•5•31•2•Updated Feb 11, 2025Feb 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 Feb 11, 2025Feb 11, 2025
epitkit
Public
R
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Other
•2•0•6•2•Updated Feb 11, 2025Feb 11, 2025
tutorials-late
Public
R
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Other
•1•2•36•0•Updated Feb 11, 2025Feb 11, 2025
tutorials-middle
Public
R
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Other
•2•3•66•2•Updated Feb 11, 2025Feb 11, 2025
tutorials-early
Public
R
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Other
•2•2•40•4•Updated Feb 11, 2025Feb 11, 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 Feb 11, 2025Feb 11, 2025
tutorials
Public
rstats pre-alpha english-language epidemic-modelling carpentries-workbench outbreak-analysis
R
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Other
•4•3•38•3•Updated Feb 11, 2025Feb 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
•932•1•23•0•Updated Feb 11, 2025Feb 11, 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•9•12•4•Updated Feb 10, 2025Feb 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•12•1•Updated Feb 10, 2025Feb 10, 2025
epiverse
Public
Meta-package for the Epiverse-TRACE R packages
r r-package epiverse
R
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Other
•0•1•0•1•Updated Feb 6, 2025Feb 6, 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
•4•43•6•3•Updated Feb 5, 2025Feb 5, 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
•12•33•50•1•Updated Feb 4, 2025Feb 4, 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•2•Updated Feb 4, 2025Feb 4, 2025
superspreading
Public
Estimation of individual level variation in transmission
epidemiology r-package disease-transmission epiverse r
R
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Other
•2•4•7•0•Updated Feb 3, 2025Feb 3, 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 Feb 3, 2025Feb 3, 2025