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workflowr

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Last updated: 2020-10-21

Checks: 2 0

Knit directory: rr_tools/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 7e6b37c

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 7e6b37c. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  README.html

Unstaged changes:
    Modified:   analysis/_site.yml

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	7e6b37c	jean997	2020-10-21	wflow_publish(“analysis/index.Rmd”)
html	2ce37af	jean997	2020-10-21	Build site.
Rmd	06a1c66	jean997	2020-10-21	wflow_publish(c(“analysis/index.Rmd”, “analysis/file_org.rmd”,
Rmd	f3d4d87	jean997	2020-10-21	add content to version_control plus some small edits
Rmd	0809fee	jean997	2020-10-21	initial structure
Rmd	fc35dfd	jean997	2020-10-21	Start workflowr project.

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Introduction

The aim of this website is to give an overview of several tools for reproducible statistical and data science research. Many of these tools will also help with workflow, organization, productivity, and your general sense of peace and well being as you go about your work.

Here are some caveats before we get going:

• This is not an exhaustive list. If you have something that you use and like I would love to know about it and add it in. Feel free to open a GitHub Issue and let me know about it!
• This website doesn’t attempt to give a thorough or exhaustive tutorial for any of the tools I cover. Instead think of it as an aggregation of useful things that have already been well documented others. I’ll do my best to supply all the links you need to get going with each thing. Please let me know if you find a broken link.
• I am mostly an R user so some of these tools are sort of R focused. Where I know about Python options I give those and many tools and practices are language agnostic.

This website was built using workflowr which I cover in the section on “Workbooks and Reports” below!

What is Reproducibility?

Content

1. File Names and Directory Structure
2. Version Control (Git)
   • Git
3. Code and Programming Practices
4. Workbooks and Reports
   • R Markdown and Sweave with knitr
   • workflowr for project organization
5. Pipelines
   • Snakemake
   • DSC for simulations

Resources

Advanced R Book by Hadley Wickham

R Packages Book by Hadley Wickham

Efficient R by Collin Gillespe and Robin Lovelace

Happy Git with R