epiverse-trace/sivirep

Data Wrangling and Automated Reports from 'SIVIGILA' source

Language: R - Size: 313 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 42 - Forks: 5

epiverse-trace/epiparameter

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

Language: R - Size: 30.1 MB - Last synced at: 2 days ago - Pushed at: 7 days ago - Stars: 36 - Forks: 13

epiverse-trace/serofoi

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies

Language: R - Size: 16.3 MB - Last synced at: 23 days ago - Pushed at: about 2 months ago - Stars: 20 - Forks: 4

epiverse-trace/vaccineff

R package with tools for estimating vaccine effectiveness and vaccine related metrics

Language: R - Size: 20.3 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 16 - Forks: 4

epiverse-trace/cfr

R package to estimate disease severity and under-reporting in real-time, accounting for reporting delays in epidemic time-series

Language: R - Size: 21.1 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 5

epiverse-trace/epiCo

R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia

Language: R - Size: 75.5 MB - Last synced at: about 23 hours ago - Pushed at: about 23 hours ago - Stars: 12 - Forks: 2

epiverse-trace/finalsize

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility

Language: R - Size: 11.2 MB - Last synced at: 20 days ago - Pushed at: 4 months ago - Stars: 11 - Forks: 7

epiverse-trace/simulist

An R package for simulating line lists

Language: R - Size: 16.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 1

epiverse-trace/epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

Language: R - Size: 23.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 5

epiverse-trace/linelist

R package for handling linelist data

Language: R - Size: 9.98 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 8 - Forks: 4

epiverse-trace/cleanepi

R package to clean and standardize epidemiological data

Language: R - Size: 17.8 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 8 - Forks: 3

epiforecasts/bpmodels

[RETIRED. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models

Language: R - Size: 5.42 MB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 7 - Forks: 7

epiverse-trace/readepi

An R package for importing epi data into R.

Language: R - Size: 22.5 MB - Last synced at: about 8 hours ago - Pushed at: 7 months ago - Stars: 6 - Forks: 5

epiverse-trace/tutorials-middle

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.

Language: R - Size: 154 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 2

epiverse-trace/superspreading

Estimation of individual level variation in transmission

Language: R - Size: 10.2 MB - Last synced at: 21 days ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

epiverse-trace/epiverse-trace.r-universe.dev

R-universe for the epiverse-trace GitHub organisation

Size: 19.5 KB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

epiverse-trace/episoap

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates

Language: R - Size: 11.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 2

epiverse-trace/tutorials-early

Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.

Language: R - Size: 20.6 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 3 - Forks: 5

epiverse-trace/blueprints

Software development blueprints for epiverse-trace

Language: SCSS - Size: 2.39 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 4

epiverse-trace/tutorials-late

Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.

Language: R - Size: 18.3 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2 - Forks: 1

epiverse-trace/epiverse-trace.github.io

Technical blog of the Epiverse-TRACE project, where we share opinions and investigations in R package development, or scientific software development more generally

Language: R - Size: 89 MB - Last synced at: 5 days ago - Pushed at: 18 days ago - Stars: 2 - Forks: 3

epiverse-trace/epiverse

Meta-package for the Epiverse-TRACE R packages

Language: R - Size: 7.46 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

epiverse-trace/epiversetheme

Language: SCSS - Size: 1.33 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1

epiverse-trace/hex-stickers

Language: JavaScript - Size: 18.2 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

epiverse-trace/scenarios

[SUSPENDED]: R package to compare epidemic scenario model outcomes.

Language: R - Size: 4.61 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1