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manuscript/1-Introduction.md

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+# 1 Introduction
+
+{type: iframe, title:1 Introduction, width:800, height:600, poster:resources/chapt_screen_images/introduction.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/introduction.html)
+
+
+

manuscript/10-References.md

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+# 10 References
+
+{type: iframe, title:10 References, width:800, height:600, poster:resources/chapt_screen_images/references.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/references.html)
+
+
+

manuscript/2-R-for-Reproducibility.md

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+# 2 R for Reproducibility
+
+{type: iframe, title:2 R for Reproducibility, width:800, height:600, poster:resources/chapt_screen_images/r-for-reproducibility.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/r-for-reproducibility.html)
+
+
+

manuscript/3-Components-of-a-reproducible-analysis.md

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+# 3 Components of a reproducible analysis
+
+{type: iframe, title:3 Components of a reproducible analysis, width:800, height:600, poster:resources/chapt_screen_images/components-of-a-reproducible-analysis.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/components-of-a-reproducible-analysis.html)
+
+
+

manuscript/4-A-Tour-of-RStudio.md

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+# 4 A Tour of RStudio
+
+{type: iframe, title:4 A Tour of RStudio, width:800, height:600, poster:resources/chapt_screen_images/a-tour-of-rstudio.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/a-tour-of-rstudio.html)
+
+
+

manuscript/5-Setting-up-your-project.md

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+# 5 Setting up your project
+
+{type: iframe, title:5 Setting up your project, width:800, height:600, poster:resources/chapt_screen_images/setting-up-your-project.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/setting-up-your-project.html)
+
+
+

manuscript/6-Reproducible-Reports.md

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+# 6 Reproducible Reports
+
+{type: iframe, title:6 Reproducible Reports, width:800, height:600, poster:resources/chapt_screen_images/reproducible-reports.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/reproducible-reports.html)
+
+
+

manuscript/7-Reproducible-Code.md

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+# 7 Reproducible Code
+
+{type: iframe, title:7 Reproducible Code, width:800, height:600, poster:resources/chapt_screen_images/reproducible-code.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/reproducible-code.html)
+
+
+

manuscript/8-Using-GitHub-in-a-workflow.md

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+# 8 Using GitHub in a workflow
+
+{type: iframe, title:8 Using GitHub in a workflow, width:800, height:600, poster:resources/chapt_screen_images/using-github-in-a-workflow.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/using-github-in-a-workflow.html)
+
+
+

manuscript/9-Software-versions.md

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+# 9 Software versions
+
+{type: iframe, title:9 Software versions, width:800, height:600, poster:resources/chapt_screen_images/software-versions.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/software-versions.html)
+
+
+

manuscript/About-the-Authors.md

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+# About the Authors
+
+{type: iframe, title:About the Authors, width:800, height:600, poster:resources/chapt_screen_images/about-the-authors.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/about-the-authors.html)
+
+
+

manuscript/About-this-Course.md

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+# About this Course
+
+{type: iframe, title:About this Course, width:800, height:600, poster:resources/chapt_screen_images/index.png}
+![](https://hutchdatascience.org/Tools_for_Reproducible_Workflows_in_R/index.html)
+
+
+

manuscript/Book.txt

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+1-Introduction.md
+2-R-for-Reproducibility.md
+quiz_ch2.md
+3-Components-of-a-reproducible-analysis.md
+quiz_ch3.md
+4-A-Tour-of-RStudio.md
+quiz_ch4.md
+5-Setting-up-your-project.md
+quiz_ch5.md
+6-Reproducible-Reports.md
+quiz_ch6.md
+7-Reproducible-Code.md
+quiz_ch7.md
+8-Using-GitHub-in-a-workflow.md
+quiz_ch8.md
+9-Software-versions.md
+quiz_ch9.md
+10-References.md
+About-this-Course.md
+About-the-Authors.md

manuscript/quiz_ch2.md

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+
+{quiz, id: why_r, attempts: 10}
+
+## What is R?
+
+{choose-answers: 4}
+? What is R?
+
+C) A language for working with data
+C) A statistical programming language
+o) A set of code that allows you to do various things
+o) Code for specifically making maps
+m) A type of programming notation
+m) A language specifically for creating websites
+
+{choose-answers: 4}
+? What does "open source" mean?
+
+C) The code is publicly available and others are able to contribute to it
+C) The code is available to the public and other people can make suggestions about it
+o) The code is only available to a select few users
+o) The code is only available to users with a GitHub account
+m) The code is hidden and can't be accessed by users
+m) The code is open for viewing but not modification
+
+{choose-answers: 4}
+? What is an R package?
+C) A set of code that can be shared between users
+C) Code that can be shared with others, either privately or publicly
+o) A way to make your code more complicated
+o) A way to make your code more efficient
+m) A way to protect your code from being seen by others
+m) A type of statistical analysis
+
+{choose-answers: 4}
+? What is one benefit of having a rich and active community in R?
+C) More resources for finding help and tutorials
+C) More opportunities to find others who can help you make your code reproducible
+o) More opportunities to make your code more complicated
+o) Less development by others needed to use R for various tasks
+m) Less support for users
+m) More difficult to find others who use R
+
+{choose-answers: 4}
+? Why is R useful for reproducibility in analyses?
+C) All of the answers
+C) Any of these answers explain why R can be useful for reproducibility
+o) It is free which means pricing is not a barrier to reproducing results with R.
+o) It has an active community who can contribute and review your code.
+m) It has an active developer community who has made lots of handy tools which aid reproducibility. 
+m) It is designed for working with data, particularly wrangling data in a reproducible way
+
+
+{/quiz}

manuscript/quiz_ch3.md

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+
+{quiz, id: components, attempts: 10}
+
+## Components of reproducibility
+
+{choose-answers: 4}
+? What does "reproducibility on a continuum" mean?
+
+C) Reproducibility that needs iterative work to improve
+C) Reproducibility that improves over time through iterations
+o) Reproducibility that is dependent on the researcher's expertise
+o) Reproducibility that is achievable only for certain types of analyses
+m) Reproducibility that can only be achieved with perfect execution
+m) Reproducibility that allows everyone everywhere to get the exact same results with your code and data
+
+{choose-answers: 4}
+? Which of the following is not a component of reproducibility?
+
+C) Efficiency
+C) Speed
+o) Transparency
+o) Clarity
+m) Accessibility
+m) Consistency
+
+{choose-answers: 4}
+? What does "open source" mean in the context of reproducibility?
+
+C) Making data and code available for anyone to access and modify
+C) Providing access to the data and code publicly where possible
+o) Providing data and code upon request by email
+o) Publishing data and code behind a paywall
+m) Storing data and code on a personal computer
+m) Not keeping the code for an analysis
+
+{choose-answers: 4}
+? Why is data sharing important in making an analysis open source?
+
+C) It helps others be able to truly reproduce the analysis by using the same data
+C) It helps other people to be able to reproduce the analysis, as they need to attempt the analysis with your data to do so
+o) It makes the analysis more complex and difficult to execute
+o) It makes it less clear what was done in our analyses
+m) It helps others to be able to publish conclusions about our data
+m) It exposes personal identifiable information to the public
+
+{choose-answers: 4}
+? Which of the following is correct about this statement - if your data has protected data that you cannot make your analysis open source or reproducible.
+
+C) These are not mutually exclusive goals! Some thoughtful planning and use of controlled access methods can ensure that all individuals' data are well protected!
+C) You can protect data and not share it, but share the code in a careful manner that does not expose details about the data.
+o) You can make your analysis reproducible but not open source
+o) You can make your analysis open source but not reproducible
+m) There are no methods that will allow you to share your methods and data in a safe way.
+m) Sharing your code is always unsafe when it comes to protected data
+
+
+{/quiz}

manuscript/quiz_ch4.md

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+
+{quiz, id: rstudio, attempts: 10}
+
+## RStudio Quiz
+
+? What is RStudio?
+
+A) A computing environment for writing code in R
+b) A specific piece of code that performs a task
+c) The Comprehensive R Archive Network
+d) The libraries needed to use R code on your computer
+
+? What is a function in R?
+
+a) An object in R
+b) A computing environment for writing code in R
+C) A specific piece of code that performs a task
+d) A Comprehensive R Archive Network
+
+? What is the purpose of an IDE in programming?
+
+a) It helps to complete what you have written
+b) It suggests package names or functions
+c) It allows you to view the output of your code
+D) All of the above
+
+? What is the Editor pane in RStudio used for?
+
+a) Looking for what objects are saved
+B) Writing code that you wish to save
+c) Both A and B
+d) Neither A nor B
+
+? What is the purpose of an R Markdown file in RStudio?
+
+a) To test code
+b) To write code in the Console
+C) To have the code for your analysis, the output from the analysis, and your written thoughts and rationale for your analysis all in one place
+d) To run code in parallel
+
+{/quiz}

manuscript/quiz_ch5.md

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+
+{quiz, id: projects, attempts: 10}
+
+## Reproducible code
+
+{choose-answers: 4}
+? Why is a well-organized project beneficial for reproducibility?
+
+C) All of the answers
+C) Any of the answers
+o) It can enable others to understand exactly what files do what
+o) It can actually make your work more efficient in the long term
+m) It can actually enable others to just take your code and run it, even with more complicated file structures
+m) It can help you and others more easily trace how specific files, data, or plots are generated
+
+{choose-answers: 4}
+? What are the goals for project organizational scheme?
+
+C) Consistent, navigable, maintainable
+C) Consistent, reduces errors, maintainable
+o) Consistent, complicated, readable
+o) Inconsistent, navigable, maintainable
+m) Consistent, complicated file structure, maintainable
+m) Inconsistent, error reduction, maintainable
+
+{choose-answers: 4}
+? What is true about project organization?
+
+C) Typically best to aim for something that is organized but not too difficult to maintain
+C) Best to strive for a schema that is organized but not too challenging to maintain
+o) Best to aim for as complicated as possible
+o) There is only one way that works best
+m) Best to aim for as organized as possible
+m) Best to aim for as easy as possible
+
+{choose-answers: 4}
+? What are some of the suggested organization tips?
+
+C) All of the answers
+C) All of the listed tips
+o) Use informative names for files
+o) Keep similar files together in a folder
+m) Include a README file that explains what all the files are
+m) number scripts in the order they are run (if more than one needs to be)
+
+{choose-answers: 4}
+? Why is the here package useful?
+
+C) All of the listed reasons
+C) All of the answers
+o) When used with an .Rproj file all paths will start from the directory that contains that file
+o) Makes it easier if you copy your files to a new computer, as you don't have to adjust paths
+m) Makes it easier for others to take your files and not have to adapt the paths to use your code
+m) Enables paths relative to the .Rproj file
+
+{/quiz}

manuscript/quiz_ch6.md

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+
+{quiz, id: rmarkdown, attempts: 10}
+
+## R Markdown Quiz
+
+? What is an R Markdown file?
+
+A) A special filetype that allows you to have your code and code output in the same file
+b) A website where people store and share their code
+c) A special filetype that allows you to mark down what code you want to keep
+d) A special filetype that can only show the output of your code
+
+? Why are R Markdown files good for reproducibility?
+a) They allow you to add descriptions around your code to describe the steps of your process
+B) They allow you to test the output of code to make sure it creates the result you expect 
+c) They allow you to share the code and the output of the code easily with others in one place
+d) All of the above
+
+? How do you create a new R Markdown file?
+a) A new R Markdown file is automatically opened when you start RStudio
+b) You right click the code in the console and save it
+C) You click on the File tab to open a new R Markdown file which opens a new pane to write and test code in
+d) You right click on the environment and save it
+
+
+? Which of the following is NOT how you test the code in an R Markdown file?
+A) You type code directly into the Console and forget to save it
+b) You press the Knit button to test all of the code within the file (and nothing outside of the file!)
+c) You use a keyboard shortcut to select and run lines of code
+d) You can press the run previous chunks button to run the code for all chunks except the current chunk
+
+? Which of the following is NOT true about R Markdown files?
+a) You can choose to hide your code or the output of the code in the final rendered report
+b) You can render the report into different kinds of file types like html or pdf by altering the YAML code at the top
+c) You can modify the aesthetics of the report
+D) R Markdown files only render the output of your code and never show your actual code 
+
+{/quiz}