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avallecam merged 2 commits into from
Jun 16, 2026
Merged

update package installation script #237

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8253635
Refactor package names in setup instructions
avallecam Jun 14, 2026
ba90074
add pak reference sentence
avallecam Jun 15, 2026
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6 changes: 4 additions & 2 deletions learners/setup.md
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Expand Up @@ -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.

Expand All @@ -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

Expand Down Expand Up @@ -174,8 +174,8 @@
if(!require("pak")) install.packages("pak")

new_packages <- c(
"epiverse-trace/readepi@readepi_no_his_spc_deps",
"cleanepi@1.1.0",
"readepi",
"cleanepi",
"reactable",
"rio",
"here",
Expand All @@ -194,6 +194,8 @@

These installation steps could ask you `? Do you want to continue (Y/n)` write `Y` and press <kbd>Enter</kbd>.

You can refer to the [{pak} reference document](https://pak.r-lib.org/reference/features.html) for more details about the advantages of using this.

::::::::::::::::::::::::::::: spoiler

### do you get an error with epiverse-trace packages?
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