Blog – Epiverse-TRACE: tools for outbreak analytics

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H5N1 (1)

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R (18)

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iteration (1)

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mpox (1)

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outbreak (1)

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cleanepi v1.1.0

new-release

We are very excited to announce the release of a new cleanepi version v1.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

Key considerations for retiring/superseding an R package

A reflection on the example of epichains and bpmodels

software lifecycles

R

R package

software design

DOI

Most of our work at Epiverse TRACE involves either developing an R package from scratch or adopting and maintaining an existing R package. In the former case…

James Mba Azam, Hugo Gruson, Sebastian Funk

superspreading v0.3.0

new-release

We are very excited to announce the release of a new superspreading version v0.3.0. This is the first version of superspreading to be on CRAN (the package can now be…

The Epiverse-TRACE development team

Licensing R packages with code and data: learnings from submitting to CRAN

R

open-source

package development

DOI

This is a follow-up blog post to the Dual licensing R packages with code and data post published in September 2024. It contains learnings from submitting epiparameter to…

Joshua Lambert, Chris Hartgerink

simulist v0.4.0

new-release

We are very excited to announce the release of a new simulist version v0.4.0. This is the first version of simulist to be on CRAN (the package can now be installed with insta…

The Epiverse-TRACE development team

epiparameter v0.4.0

new-release

We are very excited to announce the release of a new epiparameter version v0.4.0. This is the first version of epiparameter to be on CRAN (the package can now be installed…

The Epiverse-TRACE development team

How well prepared are we to rapidly analyse a new influenza pandemic? A brief perspective on analysis conducted for UK government advisory groups during COVID-19

COVID

R

real-time analysis

pandemic preparedness

H5N1

With multiple reports of influenza H5N1 cases that have no clear animal exposure, it is useful to consider what kinds of analysis would be required in the event of a new…

epiparameterDB v0.1.0

new-release

We are very excited to announce the release of a new epiparameterDB version v0.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

How we work: My first full package review

blueprints

How we work

At Epiverse-TRACE, we continuously develop packages, which risks making us (hyper)focused on the everyday changes. Feature here, bug fix there. We can call this “development…

Chris Hartgerink

vaccineff v1.0.0

new-release

We are very excited to announce the release of a new vaccineff version v1.0.0. The package offers tools for estimating vaccine effectiveness (VE) and related metrics, with…

The Epiverse-TRACE development team

epiparameter v0.3.0

new-release

We are very excited to announce the release of a new epiparameter version v0.3.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

Using LLM agents to review tutorials ‘in character’ as learners

tutorials

R

R package

Part of the Epiverse-TRACE initiative involves development of training materials that span early, middle and late stage outbreak analysis and modelling tasks. To ensure that…

Adam Kucharski, Andree Valle Campos

Dual licensing R packages with code and data

R

open-source

package development

DOI

Licenses are an important topic within open source. Without licenses, information or code can be publicly available but not legally available for reuse or redistribution.…

Joshua Lambert, Chris Hartgerink

epiparameter v0.2.0

new-release

We are very excited to announce the release of a new epiparameter version v0.2.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

Some thoughts after a trial run of GitHub’s Copilot Workspace

AI

GitHub

Copilot Workspace

R

R package

software development

DOI

GitHub recently previewed ‘Copilot Workspace’, which aims to use generative AI to assist software developers. Rather than just giving in-line suggestions, as GitHub copilot…

Joshua W. Lambert, James Mba Azam, Pratik Gupte, Adam Kucharski

Improving Ecosystem Interoperability Iteratively via Progressive Enhancement

R

interoperability

S3

progressive enhancement

ecosystem

lifecycle

object-oriented programming

DOI

We are continuing our post series on S3 object orientation and interoperability in R. We have previously discussed what makes a good S3 class and how to choose a good parent…

2024 mpox outbreak: common analytics tasks and available R tools

mpox

outbreak

outbreak analytics

DOI

There are ongoing outbreaks of mpox globally. The Democratic Republic of Congo (DRC) is so far the worst hit with a total of 7,851 cases and 384 deaths reported between…

James Azam, Hugo Gruson, Adam Kucharski

Choosing the Right Parent for R Object Classes

R

R package

object-oriented programming

S3

interoperability

DOI

I have recently published a series of blog posts on the reasons why one may want to start using object-oriented programming (and more specifically R S3 classes) to improve…

epidemics v0.4.0

new-release

We are very excited to announce the release of a new epidemics version v0.4.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

cleanepi v1.0.0

new-release

We are very excited to announce the release of a new cleanepi version v1.0.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

epichains v0.1.0

new-release

We are very excited to announce the release of a new epichains version v0.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

readepi v0.1.0

new-release

We are very excited to announce the release of a new readepi version v0.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

simulist v0.3.0

new-release

We are very excited to announce the release of a new simulist version v0.3.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

epiparameter v0.1.0

new-release

We are very excited to announce the release of a new epiparameter version v0.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

linelist v1.1.0

new-release

We are very excited to announce the release of a new linelist version v1.1.0. Here is an automatically generated summary of the changes in this version.

The Epiverse-TRACE development team

Footnotes

What is RSS? You can learn more about it with this great introductory post.↩︎