index.qmd

---
title: 'Reproducible Research with <img style="vertical-align:middle; height:35px; width: 35px; border: none;
  background: none;" src="assets/images/Rlogo.png"> and <img style="vertical-align:middle; height:35px; width: 140px;" src="assets/images/quarto-logo-trademark.svg">: Workflows for data, projects and publications'
subtitle: "A workshop presented at the [Landscape 2024 conference](https://landscape2024.org/frontend/index.php?folder_id=7393&page_id=), Berlin"
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    toc: true
    toc-title: Contents
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    number-sections: true
    number-depth: 1
citation-location: margin
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fig-align: center
---

![](assets/images/graphical_abstract_dark.png){width="70%" fig-align="center"}

This image highlights some the key concepts we will discuss in the workshop, which have been divided into seperate sections:

1.  [Background](index.qmd#sec-background): Some introductory information on why reproducible and transparent research is important.

2.  [Research projects with R](index.qmd#sec-Rprojects): Starting from the basics to develop good practice for creating research projects with R, focusing on some features of Rstudio as an Integrated Development Environment that can help ensure your work is reproducible.

3.  [Workflows for reproducibility](index.qmd#sec-workflows): Here we present three workflows of differing levels of complexity and discusses how they can be combined and which might be best given the research needs.

4.  [Quarto](index.qmd#sec-Quarto): Here we introduce the open-source scientific and technical publishing system Quarto which can be used for numerous academic activities including preparing manuscripts.

5.  [Guided Exercises](index.qmd#sec-exercises): Now it's time to get hands-on with some guided exercises to put into practice some of the concepts we have discussed.

<!-- 6.  [Resources](index.qmd#sec-resources): A collection of resources that we find particularly helpful in our own journey towards reproducible research. -->

# Background {#sec-background}

{{< include contents/intro.qmd >}}

# Research projects with R {#sec-Rprojects}

{{< include contents/Rprojects.qmd >}}

# Workflows for Reproducibility {#sec-workflows}

For this workshop we will outline three different workflows for creating reproducible research projects with R combined with other tools. We have named these workflows as follows:

1.  <img src="assets/images/Rstudio.light.svg" style="vertical-align:middle; height:1em;"/> to <img src="assets/images/Zenodo.dark.svg" style="vertical-align:0%; height:0.85em;"/> pipeline

2.  Containerization with <img src="assets/images/Docker.dark.svg" style="vertical-align:0%; height:1.25em;"/>

3.  Version control with <img src="assets/images/Github.light.svg" style="vertical-align:0%; height:0.75em;"/>

These workflows are inter-related in the sense that 2. and 3. build upon elements of the first and indeed the techniques of the latter workflows can also be combined together. The workflows differ in the level of reproducibility they ensure but the trade-off for better reproducibility is increased complexity. As such we would suggest that the most reproducible workflow may not always be the most appropriate to implement dependent on the needs of your research project and the capabilities of the collaborators involved.

Of course, these workflows are by no-means the only way of doing things and indeed we would actively encourage you to expand upon them in developing your own preferred approach.

## <img src="assets/images/Rstudio.dark.svg" style="vertical-align:middle; height:1.5em;"/> project to <img src="assets/images/Zenodo.light.svg" style="vertical-align:0%; height:0.85em;"/> pipeline {#sec-zenodo_workflow}

{{< include contents/Zenodo_workflow.qmd >}}

## Containerization with <img src="assets/images/Docker.light.svg" style="vertical-align:0%; height:1.25em;"/> {#sec-docker_workflow}

{{< include contents/Docker_workflow.qmd >}}

## Version control with <img src="assets/images/Github.dark.svg" style="vertical-align:0%; height:0.75em;"/> {#sec-git_workflow}

{{< include contents/Git_workflow.qmd >}}

# Quarto {#sec-Quarto}

{{< include contents/Quarto_intro.qmd >}}

# Guided excercises {#sec-exercises}

Now it's time to get hands on with some guided exercises that will let you put into practice the [three workflows for reproducible research](index.qmd#sec-workflows) that we have introduced as well as writing a academic manuscript using [Quarto](index.qmd#sec-Quarto). Each exercise is available to download as a PDF if you prefer to view the instructions offline and the files required for each are available to download at the start of each exercise.

{{< include exercises/Rproj-Zenodo_exercise.qmd >}}

{{< include exercises/Docker_exercise.qmd >}}

{{< include exercises/Git_exercise.qmd >}}

{{< include exercises/Quarto-manuscript_exercise.qmd >}}

<!-- # Resources {#sec-resources} -->

{{< include contents/Resources.qmd >}}