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update setup packages #35

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merged 3 commits into from
Mar 30, 2024
Merged

update setup packages #35

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77d7ce7
clean entry sentence
avallecam Mar 30, 2024
5c335a4
add incidence2 package as prep for rt episode
avallecam Mar 30, 2024
213c40c
fix writing using grammarly
avallecam Mar 30, 2024
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10 changes: 6 additions & 4 deletions learners/setup.md
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Expand Up @@ -4,17 +4,17 @@ title: Setup

## Motivation

**Outbreaks** appear with different diseases and in different contexts, but what all of them have in common are the key public health **questions** ([Cori et al. 2017](https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371#d1e605)). Common questions also require common data analysis **tasks**.
**Outbreaks** appear with different diseases and in different contexts, but what all of them have in common is the key public health **questions** ([Cori et al. 2017](https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371#d1e605)). We can relate these key public health questions to outbreak data analysis **tasks**.

Epiverse-TRACE's aim is to provide an software ecosystem for [**outbreak analytics**](reference.md#outbreakanalytics) 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.
Epiverse-TRACE aims to provide a software ecosystem for [**outbreak analytics**](reference.md#outbreakanalytics) 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.

### Epiverse-TRACE tutorials

The tutorials are built around the workflow of outbreak analysis split into three stages: **Early tasks**, **Middle tasks** and **Late tasks**.
The tutorials are built around an outbreak analysis pipeline 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.
Each task has its tutorial website. Each tutorial website consists of a set of episodes.

| [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/) |
|---|---|---|
Expand Down Expand Up @@ -108,6 +108,7 @@ if(!require("pak")) install.packages("pak")
new_packages <- c(
"EpiNow2",
"epiverse-trace/epiparameter",
"incidence2",
"tidyverse"
)

Expand All @@ -123,6 +124,7 @@ When the installation has finished, you can try to load the packages by pasting
```r
library(EpiNow2)
library(epiparameter)
library(incidence2)
library(tidyverse)
```

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