Note: This lesson is currently orphaned. People interested in taking a lead on further developing it are welcome to step forward. Post an issue expressing your interest and where you would like this to go, or file a pull request.

##Purpose To teach students to VERB [and VERB] the way that organization can be used to inform themselves and others about the project throughout its life

##Motivation Why is it worth organizing? Graph Illustrating effort verse time. Yes, this is a little painful, but think of how painful it will be during publication process.

![graph] (https://raw.githubusercontent.com/tracykteal/shell-genomics/master/img/gvng.jpg)

##Overview of exercises

1. get set of files (raw data, scripts, overall .Rmd) for gapminder all in one directory

• raw data: raw1.csv, raw2.csv, raw3.csv
• scripts to clean the data: clean1.R, ..., clean7.R
• overall Rmd: project.Rmd

Run the whole thing to produce clean data (clean.csv) and output files (project.md, project.html, sweden.png).

2. How to organize these files? Students work on this in small groups, to organize into subfolders (separating code from data).

   Come back together to discuss students' solutions; point them toward a modified version of Bill Nobel's approach.

    project.Rmd
    doc/paper/
    data/raw/raw1.csv
    data/raw/raw2.csv
    data/raw/raw3.csv
    data/clean/clean.csv
    code/clean1.R
    ...
    code/clean7.R
    results/project.md
    results/project.html
    results/figure/sweden.png
   

3. Discussion of paths, particularly regarding relative vs absolute paths.

   • what we had to change (paths) to redirect files
   • If you gave to friend how do those path names effect that?
   • importance of absolute vs relative paths
   • what if you were to move this to a new computer?
   • Working directory

4. Exercise: we need to do the actual moving around, and we need to

   • go into the code/*.R files and change the paths to the raw and clean data
   • go into the project.Rmd file to change the paths to clean*.R and data/clean/clean.csv.
   • change project.Rmd to send figure to results/figure/; change preferences for knitr to send output to results/.

(Potentially skip this exercise and provide them with a reorganized version.)

5. Add some new analysis to the main Rmd file, and re-run.

6. metadata exercise: what metadata will you want to record in order to explain what files are what, and which ones produce which others

   • README file explaining everything

     • for yourself, coming back to this 6 months from now
     • for a collaborator

7. versions: how do they keep track of versions of things? (discussion in small groups and then come back together)

   • periodic zipping of project directory
   • Time Machine or other backup system
   • project on dropbox
   • github

8. (Lecture interlude: demonstration of GitHub)