Getting started

Our aim is to help change how analytics are used in the global infectious disease response, moving towards integrated, generalisable and scalable community-driven software.

Quickstart

To install and load all the latest stable versions, as released on CRAN, install the epiverse meta-package as follows:

pak::pak('epiverse-trace/epiverse')
library(epiverse)

# Loading required package: cfr
# Loading required package: cleanepi
# Loading required package: finalsize
# Loading required package: linelist

This will allow you to start using these packages in your analyses. You can then follow the quick starts for the respective packages:

• cfr - quick start
• cleanepi - quick start
• finalsize
• linelist

Roadmap

More packages are in development, but not yet with a stable release. our roadmap is to cover early through late tasks :

Epiverse-TRACE packages

We are developing the following packages. These are built on methods and analysis that have informed epidemic response to infections including cholera, COVID, dengue, diphtheria, Ebola, influenza, and Zika.

Early tasks

Middle tasks

Late tasks

Import data

Access and manipulate Colombian data

Clean imported data

Simulate outbreak data

Tag and validate individual data

Access epidemiological parameters

Generate automated report for SIVIGILA data

Use curated pipelines

Estimate disease severity

Estimate force of infection from serology

Tools for vector-borne infections

Simulate vector-borne outbreaks

Simulation and analysis of transmission chains

Analysis of transmission variation

Calculate epidemic final size

Simulate epidemic dynamics

Analyze vaccine efficacy

Install development versions using the following command in R:

pak::pak('epiverse-trace/<package-name>')

This will install the development version for you to try out. Please note that these may change until they have a stable release.