Scientific reproducibility: What is it for?

Figure 1

PhD Comics cartoon

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Nature Report - 2016

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Science is not a miracle

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How science should be

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Good Practices for Managing Projects in RStudio

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directory tree

Navigating RStudio and Quarto Documents

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RStudio layout

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RStudio layout with .R file open

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Name new .qmd file

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.qmd new file generic template

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Add image source editor

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Note that both the visual and the source editors offer the option to display an outline of your document image which makes it easier to navigate long documents.

Working with projects in RStudio

Figure 1

new r project options

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quarto projects

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New directory

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Then, to use version control, make sure to check the “Create a git repository” box as highlighted in this screenshot: new project w/ version control

Figure 5

existing project

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version controlled The final option is to continue a version-controlled project. This is the option we will do for our workshop.

Figure 7

Git or Subversion

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continue project from GitHub

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GitHub

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fork on GitHub

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copy GitHub repository url

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start my R project

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Git not detected on system path

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To set it up, we need to go to Tools > Global Options Global Options Git/SVN setup

Introduction to Working with Quarto documents

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Quarto Workflow

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yaml highlighted in document

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qmd template text

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Render html output

Writing and Styling Quarto Documents

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Fig. 6.1 - Toolbar

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Fig. 6.2 - Menu

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Clear Formatting Option

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Fig. 6.3 - Shortcuts

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Text with borders rendered

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Two columns rendered

Adding Code to Quarto Documents

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auto create code chunk

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blank qmd code chunk

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run from code chunk

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run code menu

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directory error code chunk

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path error details

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Code Chunk Plot Preview

Rendering and Customizing Code Outputs

Figure 1

Heart rate code no options for code chunk

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code chunk label

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Error due to wrong order

Advanced Code Chunk Options

Figure 1

Project Options

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Quarto yml project setting

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basic code chunk

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03-HR-analysis.R externally sourced in Qmd Document

Bibliography, Citations and Cross-Referencing

Figure 1

Citation Window

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references.bib

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Salviary Cortisol

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DOI Lookup

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Inserting cross-referencing

Using Git in RStudio

Figure 1

Git menu bar

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git environment panel

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git add commit workflow

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git panel add

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git panel icons

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commit in RStudio

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  • Open the .gitignore file by double-clicking on it in the file view pane; on a new line, add data/. Save the file, and don’t forget to commit it. .gitignore file

    • Figure 8

  • Click on the settings gear in the Git tab of the environment pane. Click on gitignore. On a new line, add data and click save. Don’t forget to commit the .gitignore file. .gitignore in git pane

    • Collaborating via GitHub

    Figure 1

    PAT options on GitHub

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    Copy Repo URL from GitHub

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    RSTudio Project Options Git/SVN

    Managing Dependencies in R/RStudio

    Publishing your project

    Figure 1

    Publish button in RStudio

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    Publish to RPubs or RStudio Connect

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    Confirm Publish to RPubs

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    Quarto Pub Publish command

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    Quarto Pub Publish Example

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    RStudio output formats

    Figure 7

    Journal-Templates

    Creating and sharing reproducible environments with renv

    Figure 1

    Understanding how the R System works

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    Project local library

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    Renv for new project

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    Environments

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    Anatomy of a renv.lock file

    Figure 6

    Renv