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

Figure 1

directory tree

Navigating RStudio and Quarto Documents

Figure 1

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 make 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

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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

Figure 8

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

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  • Menu bar (Tools menu) Git menu bar

    • Figure 16

  • Environment/History pane git environment panel

    • Figure 17

    git add commit workflow

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    git panel add

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    git panel add

    Figure 20

    git panel icons

    Figure 21

    commit in RStudio

    Figure 22

  • 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 23

  • 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

    • Introduction to Working with Quarto documents

    Figure 1

    Quarto Workflow

    Figure 2

    yaml highlighted in document

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    qmd template text

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    Render html output

    Writing and Styling Qmd Documents

    Figure 1

    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

    Figure 1

    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 & Customizing Code Outputs

    Figure 1

    Heart rate code no options for code chunk

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    code chunk label

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  • fig-alt: (NULL; character) The alternative text to be used in the alt attribute of the tags of figures in HTML output. By default, the chunk option fig-cap will be used as the alternative text if provided.

    • Figure 4

    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

    Figure 4

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

    Bibliography, Citations & Cross-Referencing

    Figure 1

    Citation Window

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    references.bib

    Figure 3

    Salviary Cortisol

    Figure 4

    DOI Lookup

    Figure 5

    Inserting cross-referencing

    Using Git in RStudio

    Figure 1

  • Menu bar (Tools menu) Git menu bar

    • Figure 2

  • Environment/History pane git environment panel

    • Figure 3

    git add commit workflow

    Figure 4

    git panel add

    Figure 5

    git panel icons

    Figure 6

    commit in RStudio

    Figure 7

  • 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

    Figure 2

    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

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    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