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avallecam committed Oct 30, 2024
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Expand Up @@ -6,50 +6,3 @@ This is an [Epiverse-TRACE][epiversetrace] tutorial built with [The Carpentries

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

## Epiverse-TRACE tutorials

The Epiverse-TRACE tutorials are training materials for Outbreak Analysis tasks aimed at [learners](../profiles.md) who are willing to achieve basic competence in modelling and analytics.

The tutorials are built around the workflow of outbreak analysis split into three stages : early tasks, middle tasks and late tasks.

![An overview of the tutorial topics](https://epiverse-trace.github.io/task_pipeline-minimal.svg)

Each task has its own tutorial website. Task topics consist of one or more episodes.

## Workshop overview

| [Early task tutorials](https://epiverse-trace.github.io/tutorials-early/) | [Middle task tutorials](https://epiverse-trace.github.io/tutorials-middle) | [Late task tutorials](https://epiverse-trace.github.io/tutorials-late/) |
|---|---|---|
| Reading and cleaning case data | Real-time analysis and forecasting | Scenario modelling |
| Read and clean linelist data, Access delay distributions, and Estimate transmission metrics. | Forecast cases, Estimate severity, and Estimate superspreading. | Simulate disease spread and Investigate interventions. |

| Tutorial | Overview |
| ---------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ |
| [Reading and cleaning data for outbreak analytics with R](https://epiverse-trace.github.io/tutorials-early/) | Read and clean linelist data, reuse delay distributions, and estimate transmission metrics. |
| [Real-time analysis and forecasting for outbreak analytics with R ](https://epiverse-trace.github.io/tutorials-middle/) | Quantify transmissibility, forecast cases, and estimate delay-adjusted severity measurements |
| [Scenario modelling for outbreak analytics with R](https://epiverse-trace.github.io/tutorials-late/) | Generate disease spread model simulations, and investigate interventions. |


Each tutorial contain a set of episodes. Each episode contains:

+ **Overview** : describes what questions will be answered and what are the objectives of the episode.
+ **Prerequisites**: describes what episodes/packages need to be covered before the current episode.
+ **Example R code** : work through the episodes on your own computer using the example R code.
+ **Challenges** : complete challenges to test your understanding.
+ **Explainers** : add to your understanding of mathematical and modelling concepts with the explainer boxes.
+ **Glossary** : contain terms you may be unfamiliar with.


:::::::::::::::::::::::::::: prereq

This course assumes intermediate R knowledge. This workshop is for you if:

- You can use the magrittr pipe `%>%` and/or native pipe `|>`
- You are familiar with functions from `{dplyr}`, `{tidyr}`, and `{ggplot2}`
- You can read data into R, transform and reshape data, and make a wide variety of graphs

We expect participants to have some exposure to basic Statistical, Mathematical and Epidemic theory concepts, but NOT intermediate or expert familiarity with modeling.

::::::::::::::::::::::::::::

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