Data analysis files
- Data - raw and processed
- Figures - exploratory and final
- R code - raw/unused scripts, final scripts, R Markdown files
- Text - README files, text of analysis/report
Raw Data
- should be stored in your analysis folder
- if accessed from the web, include the URL, description, and data accessed in the README
Processed Data
- should be named so it is easy to see which script generated the data
- the processing script - processed data mapping should occur in the README
- should be tidy
Exploratory figures
- made during the course of your analysis, not necessarily part of your final report
- do not need to be 'pretty'
Final figures
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- usually a small subset of the original figures
- axes/colors set to make the figure clear
- possibly multiple panels
Raw scripts
- may be less commented (but comments help you!)
- may be multiple versions
- may include analyses that are later discarded
Final scripts
- clearly commented - small comments liberally (what, why, when, how), bigger commented blocks for whole sections
- include processing details
- only analyses that appear in the final write-up
R Markdown Files
- can be used to generate reproducible reports
- text and R code are integrated
- very easy to create in Rstudio
Readme files
- Not necessary if you use R Markdown
- should contain step-by-step instructions for analysis
- Example: http://github.com/jtleek/swfdr/blob/master/REAMDE.md
Text of the document
- should include a title. introduction (motivation), methods (statistics you used), results (including measures of uncertainty), and conclusions (including potential problems)
- should tell a story
- should not include every analysis you performed
- references should be included for statistical methods