Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 3 additions & 5 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->
<!-- Render with: rmarkdown::render("README.Rmd") -->

```{r, include = FALSE}
knitr::opts_chunk$set(
Expand Down Expand Up @@ -41,15 +42,12 @@ Lesson content is published with a [CC-BY license](LICENSE.md).

Current maintainers of these tutorials are:

- [Andree Valle-Campos](https://github.com/avallecam/) (Content)
- [Hugo Gruson](https://github.com/Bisaloo/) (Infrastructure)
- [Andree Valle-Campos](https://github.com/avallecam/)

<!--
Former maintainers:

- [Andree Valle-Campos](https://github.com/avallecam/)
- [Hugo Gruson](https://github.com/Bisaloo/)

-->

<!--## Acknowledgements-->

Expand Down
17 changes: 11 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ the pages, see the [Introduction to The Carpentries
Workbench](https://carpentries.github.io/sandpaper-docs/).

<!-- ## Support -->

<!-- Please see our [Getting help guide](/.github/SUPPORT.md) for support. -->

## License
Expand All @@ -45,6 +46,11 @@ Current maintainers of these tutorials are:

- [Andree Valle-Campos](https://github.com/avallecam/)

Former maintainers:

- [Hugo Gruson](https://github.com/Bisaloo/)

<!--## Acknowledgements-->

## Related

Expand Down Expand Up @@ -77,20 +83,19 @@ use it](https://citation-file-format.github.io/).)

To cite these tutorials in publications use:

Minter A, Degoot A (2025). "Epiverse-TRACE Tutorials Late: Scenario
modelling for outbreak analytics with R."
Minter A, Degoot A, Valle-Campos A, Gruson H, Bah B, Funk S, Eggo R, Kucharski A (2026). "Epiverse-TRACE Tutorials Late: Scenario modelling for outbreak analytics with R."
<https://epiverse-trace.github.io/tutorials-late/>.

A BibTeX entry for LaTeX users is:

@Misc{minter_etall:2025,
@Misc{minter_etall:2026,
title = {Epiverse-TRACE Tutorials Late: Scenario modelling for outbreak analytics with R},
author = {Amanda Minter and Abdoelnaser Degoot},
year = {2025},
author = {Amanda Minter and Abdoelnaser Degoot and Andree Valle-Campos and Hugo Gruson and Bubacarr Bah and Sebastian Funk and Rosalind Eggo and Adam Kucharski},
year = {2026},
url = {https://epiverse-trace.github.io/tutorials-late/},
abstract = {The Epiverse-TRACE initiative aims to provide a software ecosystem for outbreak analytics with integrated, generalisable and scalable community-driven software. We support the development of R packages, make the existing ones interoperable for the user experience, and stimulate a community of practice. In the outbreak analytics curriculum, we built three tutorials around an outbreak analysis pipeline split into three stages: Early, Middle, and Late tasks. Early tasks include reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves. Middle tasks host real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from incidence data, superspreading from line list and contact data, and simulating transmission chains. Late tasks include accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.},
keywords = {outbreak-analytics,scenario-modelling,contact-matrix,non-pharmaceutical-interventions,vaccination,disease-burden,carpentries-workbench,rstats,english-language},
version = {v2025-03-11},
version = {v2026-07-23},
}

## Contact
Expand Down
2 changes: 1 addition & 1 deletion config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ keywords: 'epidemic models, interventions'

# Life cycle stage of the lesson
# possible values: pre-alpha, alpha, beta, stable
life_cycle: 'pre-alpha'
life_cycle: 'beta'

# License of the lesson materials (recommended CC-BY 4.0)
license: 'CC-BY 4.0'
Expand Down
2 changes: 1 addition & 1 deletion index.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
site: sandpaper::sandpaper_site
---

This is an [Epiverse-TRACE][epiversetrace] tutorial built with [The Carpentries Workbench][workbench].
This is an [Epiverse-TRACE][epiversetrace] tutorial.

[epiversetrace]: https://epiverse-trace.github.io/
[workbench]: https://carpentries.github.io/workbench/
Loading