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add cleanepi dependency for report #190

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2 changes: 2 additions & 0 deletions learners/setup.md
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@
Our tutorials are built around an outbreak analysis pipeline split into three stages: **Early tasks**, **Middle tasks** and **Late tasks**. The outputs of tasks completed in earlier stages commonly feed into the tasks required for later ones.


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

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[image missing alt-text]: https://epiverse-trace.github.io/task_pipeline-minimal.svg

Each task has its tutorial website and each tutorial website consists of a set of episodes covering different topics.

@@ -36,7 +36,7 @@

Our strategy is to gradually incorporate specialised **R packages** into a traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks.

![In **R**, the fundamental unit of shareable code is the **package**. A package bundles together code, data, documentation, and tests and is easy to share with others ([Wickham and Bryan, 2023](https://r-pkgs.org/introduction.html))](episodes/fig/pkgs-hexlogos-2.png)

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[image missing alt-text]: episodes/fig/pkgs-hexlogos-2.png

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

@@ -111,6 +111,7 @@

new_packages <- c(
"cleanepi",
"reactable",
"rio",
"here",
"DBI",
@@ -203,6 +204,7 @@
# for episodes on read, clean, validate and visualize linelist

library(cleanepi)
library(reactable)
library(rio)
library(here)
library(DBI)