Last updated: 2018-10-30

workflowr checks: (Click a bullet for more information)

  • ✖ R Markdown file: uncommitted changes The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

  • ✔ Environment: empty

    Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

  • ✔ Seed: set.seed(20181015)

    The command set.seed(20181015) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

  • ✔ Session information: recorded

    Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

  • ✔ Repository version: a71b71a

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/data/
    Ignored:    analysis/package.Rmd
    Ignored:    assets/
    Ignored:    docs/.DS_Store

Untracked files:
    Untracked:  analysis/paper.Rmd
    Untracked:  docs/assets/Boettiger-2018-Ecology_Letters.pdf
    Untracked:  docs/assets/Packaging-Data-Analytical Work-Reproducibly-Using-R-and-Friends.pdf

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/analysis.Rmd
    Modified:   analysis/create-compendium.Rmd
    Modified:   analysis/index.Rmd
    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.
Expand here to see past versions:
    File Version Author Date Message
    html 921a7f8 annakrystalli 2018-10-30 commit docs
    Rmd f1468ac annakrystalli 2018-10-30 commit Rmd

Create analysis

✔ Adding bookdown to Imports
✔ Creating 'analysis' directory and contents
✔ Creating 'analysis'
✔ Creating 'analysis/paper'
✔ Creating 'analysis/figures'
✔ Creating 'analysis/templates'
✔ Creating 'analysis/data'
✔ Creating 'analysis/data/raw_data'
✔ Creating 'analysis/data/derived_data'
✔ Creating 'references.bib' from template.
✔ Creating 'paper.Rmd' from template.

Next, you need to:  ↓ ↓ ↓ ↓ 
● Write your article/report/thesis, start at the paper.Rmd file
● Add the citation style library file (csl) to replace the default provided here, see https://github.com/citation-style-language/
● Add bibliographic details of cited items to the 'references.bib' file
● For adding captions & cross-referencing in an Rmd, see https://bookdown.org/yihui/bookdown/
● For adding citations & reference lists in an Rmd, see http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html

Note that:
⚠ Your data files are tracked by Git and will be pushed to GitHub

This adds the following files:

├── analysis
│   ├── data
│   │   ├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
│   │   ├── derived_data
│   │   └── raw_data
│   ├── figures
│   ├── paper
│   │   ├── paper.Rmd
│   │   └── references.bib
│   └── templates
│       ├── journal-of-archaeological-science.csl
│       ├── template.Rmd
│       └── template.docx
├── man
└── rrcompendium.Rproj

Let’s inspect

paper.Rmd

paper.Rmd is ready to write in and render with bookdown. It includes:

  • a YAML header that identifies the references.bib file and the supplied csl file (Citation Style Language) to style the reference list) - a colophon that adds some git commit details to the end of the document. This means that the output file (HTML/PDF/Word) is always traceable to a specific state of the code.

references.bib

The references.bib file has just one item to demonstrate the format. It is ready to insert more reference details.

We can replace the supplied csl file with a different citation style from https://github.com/citation-style-language/

data/

Move gillespie.csv from the materials you downloaded in rrtools-wkshp-materials-master/ to analysis/data/raw_data/ in rrcompendium

Your data folder should now look like this:

analysis/data
├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
├── derived_data
└── raw_data
    └── gillespie.csv

Session information

This reproducible R Markdown analysis was created with workflowr 1.1.1