Epiverse-TRACE

All

59 repositories

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 Jan 9, 2025Jan 9, 2025
simulist
Public
An R package for simulating line lists
r epidemiology r-package outbreaks linelist epiverse
R
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Other
•1•5•8•1•Updated Jan 9, 2025Jan 9, 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•3•Updated Jan 8, 2025Jan 8, 2025
epiCo
Public
R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia
colombia r-package demographics decision-support spatio-temporal-analysis vector-borne-diseases epiverse outbreak-analysis r
R
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Other
•1•12•9•1•Updated Jan 8, 2025Jan 8, 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•17•28•4•Updated Jan 8, 2025Jan 8, 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
•11•33•49•0•Updated Jan 8, 2025Jan 8, 2025
etdashboard
Public
Developer dashboard for a universe overview of Epiverse-TRACE packages
R
•0•1•0•0•Updated Jan 8, 2025Jan 8, 2025
etstats
Public
r r-package organisation-tool
R
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Creative Commons Zero v1.0 Universal
•0•1•2•0•Updated Jan 7, 2025Jan 7, 2025
tutorials-middle
Public
R
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Other
•2•3•66•2•Updated Jan 7, 2025Jan 7, 2025
epitkit
Public
R
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Other
•2•0•6•1•Updated Jan 7, 2025Jan 7, 2025
epimodelac
Public
Training materials for the epimodelac workshop
r rstats carpentries-workbench
R
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Other
•4•8•11•2•Updated Jan 7, 2025Jan 7, 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 Jan 7, 2025Jan 7, 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 Jan 7, 2025Jan 7, 2025
tutorials-late
Public
R
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Other
•1•2•38•4•Updated Jan 7, 2025Jan 7, 2025
tutorials-early
Public
R
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Other
•2•2•40•4•Updated Jan 7, 2025Jan 7, 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
•929•1•23•0•Updated Jan 7, 2025Jan 7, 2025
safeframe
Public
Tagging, validating, and safeguarding data to help harden data pipelines.
R
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Other
•0•0•8•3•Updated Jan 6, 2025Jan 6, 2025
epiparameterDashboard
Public
Explore the database of epidemiological parameters provided by the {epiparameterDB} package
R
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Other
•0•0•1•1•Updated Jan 3, 2025Jan 3, 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 Jan 2, 2025Jan 2, 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 Jan 2, 2025Jan 2, 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•7•14•4•Updated Jan 1, 2025Jan 1, 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•17•3•Updated Jan 1, 2025Jan 1, 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
•3•16•1•1•Updated Jan 1, 2025Jan 1, 2025
climateR0
Public
R
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Other
•0•0•4•7•Updated Jan 1, 2025Jan 1, 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
•3•8•17•2•Updated Jan 1, 2025Jan 1, 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•23•5•Updated Jan 1, 2025Jan 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
R
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Other
•4•13•10•3•Updated Jan 1, 2025Jan 1, 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•26•0•Updated Dec 19, 2024Dec 19, 2024
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•9•3•Updated Dec 10, 2024Dec 10, 2024
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 Dec 6, 2024Dec 6, 2024