Big update to README, regarding plans for flow of exercises

README.md

@@ -3,37 +3,73 @@ To teach students to VERB [and VERB] the way that organization can be used to in
 
 ##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 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
-- get a bunch of files (raw data, scripts, overall .Rmd): run the whole thing to produce clean data and output files
-- now have a bunch of files (raw and clean data, scripts, results); how to organize them?
-    - README file explaining everything
-    - organize into subfolders (separating code from data)
-
-- Potentially re-run .Rmd: have them actively reorganize and change paths
-- Get a version with files reorganized; add some new analysis to the main Rmd file
-- Lecture interlude: 
-      - If you gave to friend how do those path names affect that?
+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
-
-- metadata exercise: what metadata will you want to record in order to explain what files are what, and which ones produce which others
+
+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
-      
-- versions: how do they keep track of versions of things? (discussion in small groups and then come back together)
+
+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
-
-- (Lecture interlude: demonstration of GitHub)      
-
 
+8. (Lecture interlude: demonstration of GitHub)