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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.
Apr 21, 2025
The Epiverse-TRACE development team
 

Integration testing in Epiverse-TRACE

Robust interoperability of R packages
open-source
R
R package
testing
interoperability
ecosystem
In Epiverse-TRACE we develop a suite of R packages that tackle predictable tasks in infectious disease outbreak response. One of the guiding software design principles we…
Apr 14, 2025
Joshua W. Lambert
 

simulist v0.5.0

new-release
We are very excited to announce the release of a new simulist version v0.5.0. Here is an automatically generated summary of the changes in this version.
Mar 26, 2025
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…
Feb 3, 2025
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…
Jan 28, 2025
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…
Jan 20, 2025
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…
Jan 10, 2025
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…
Jan 8, 2025
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…
Dec 23, 2024
Adam Kucharski
 

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.
Dec 18, 2024
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…
Dec 9, 2024
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…
Dec 2, 2024
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.
Nov 21, 2024
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…
Nov 18, 2024
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.…
Sep 23, 2024
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.
Jul 22, 2024
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…
Jul 15, 2024
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…
Jul 5, 2024
Hugo Gruson
 

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…
Jul 4, 2024
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…
Jun 26, 2024
Hugo Gruson
 

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.
Jun 24, 2024
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.
Jun 17, 2024
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.
Jun 10, 2024
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.
Jun 10, 2024
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.
Jun 3, 2024
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.
May 30, 2024
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.
Feb 28, 2024
The Epiverse-TRACE development team
 

epidemics v0.1.0

new-release
We would like to announce the realease on GitHub of version 0.1.0 of epidemics.
Feb 27, 2024
The Epiverse-TRACE development team
 

simulist v0.2.0

new-release
We are very excited to announce the release of a new simulist version v0.2.0. Here is an automatically generated summary of the changes in this version.
Feb 23, 2024
The Epiverse-TRACE development team
 

New team member: Chris Hartgerink

Team
In January, I joined Epiverse as part of my new role as Senior Software Engineer at data.org. In the weeks since, I have been able to already meet a lot of members of the…
Feb 15, 2024
Chris Hartgerink
 

Things that can go wrong when using renv

R
reproducibility
renv
DOI
Throughout the Epiverse project, we use the renv R package to ensure reproducibility of the training materials and the pipelines we are providing. But we sometimes get…
Jan 31, 2024
Hugo Gruson
 

superspreading v0.2.0

new-release
We are very excited to announce the release of a new superspreading version v0.2.0. Here is an automatically generated summary of the changes in this version.
Jan 29, 2024
The Epiverse-TRACE development team
 

simulist v0.1.0

new-release
We are very excited to announce the release of a new simulist version v0.1.0. Here is an automatically generated summary of the changes in this version.
Jan 9, 2024
The Epiverse-TRACE development team

Using benchmarking to guide the adoption of dependencies in R packages

An example with cli
benchmarking
R
cli
R package
software architecture
R package developers often have to take on dependencies for various reasons. Dependencies are external packages that provide extra functionalities or features to another…
Nov 22, 2023
James Mba Azam
 

cfr v0.1.0

new-release
We are very excited to announce the release of a new cfr version v0.1.0. Here is an automatically generated summary of the changes in this version.
Nov 22, 2023
The Epiverse-TRACE development team
 

bpmodels v0.3.1

new-release
We are very excited to announce the release of a new bpmodels version v0.3.1. Here is an automatically generated summary of the changes in this version.
Nov 6, 2023
The Epiverse-TRACE development team
 

Lesser-known reasons to prefer apply() over for loops

R
functional programming
iteration
readability
good practices
tidyverse
The debate regarding the use of for loops versus the apply() function family (apply(), lapply(), vapply(), etc., along with their purrr counterparts: map(), map2(), map_lgl()…
Nov 2, 2023
Hugo Gruson
 

linelist v1.0.0

new-release
We are very excited to announce the release of a new linelist version v1.0.0. Here is a automatically generated summary of the changes in this version.
Oct 19, 2023
The Epiverse-TRACE development team
 

System Dependencies in R Packages & Automatic Testing

package development
R
R package
continuous integration
system dependencies
This post has been cross-posted on the R-hub blog, and the R-hub blog maintainers have contributed to the review and improvement of this post.
Sep 26, 2023
Hugo Gruson
 

Communicating development stages of open-source software

open-source
R
R package
versioning
lifecycles
community
Software is not immediately stable when being developed. It undergoes design changes, changes to the user interface (application programming interface, API), and features…
Jul 18, 2023
Joshua W. Lambert
 

Sharing the C++ Code of an Rcpp Package

code sharing
R
R package
Rcpp
interoperability
package development
Using the {Rcpp} package is the dominant method for linking the usability of R with the speed of C++, and can be used to write R packages that are fast and easy to use for…
Jun 5, 2023
Pratik Gupte
 

Extending Data Frames

Creating custom classes and {dplyr} compatibility
data frame
R
R package
interoperability
S3
tidyverse
object-oriented programming
R is a commonly used language for data science and statistical computing. Foundational to this is having data structures that allow manipulation of data with minimal effort…
Apr 12, 2023
Joshua W. Lambert

Situation report: Location: Banjul, The Gambia. Pathogen: novel respiratory disease. Background: index case travelled to London in Dec 2022. 85 symptomatic individuals identified in February 2023 are under investigation. Modified data: linelist: added travel history column, added imported case column, added id column, added missing cases, introduced errors; contact database: added missing cases and introduced errors. Questions: 1. What are the most affected groups? 2. What are the epidemiological characteristics of infection? 2. What is the level of individual variation of transmission? 3. How is the outbreak likely to develop over the next weeks? 4. What public health measures are required to contain it?

What Should the First 100 Lines of Code Written During an Epidemic Look Like?

outbreak analytics
100 days workshop
participatory research
This vignette summarises the findings from the 100 days and 100 lines of code workshop, hosted in December 2022 by Epiverse-TRACE.
Mar 9, 2023
Carmen Tamayo

Convert Your R Function to an S3 Generic: Benefits, Pitfalls & Design Considerations

R
R package
object-oriented programming
S3
interoperability
To build a tight and well-integrated data pipeline, it may be desirable to rely on object orientation (OO) to automatically pass valuable information from one step to the…
Feb 20, 2023
Hugo Gruson
 

Improving the C++ Code Quality of an Rcpp Package

code quality
R
R package
Rcpp
good practices
continuous integration
The R package development ecosystem includes packages such as {lintr} and {styler} that can help to check code style, and to format R code.
Feb 16, 2023
Pratik Gupte

Ensuring & Showcasing the Statistical Correctness of your R Package

code quality
R
R package
testing
continuous integration
good practices
We’re evolving in an increasingly data-driven world. And since critical decisions are taken based on results produced by data scientists and data analysts, they need to be…
Feb 13, 2023
Hugo Gruson
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