Latest changes: ready for next round of editing

.gitignore

@@ -7,4 +7,5 @@
 *.fdb_latexmk
 *.log
 *.out
-
+workflow_cache
+.Rhistory

README.md

@@ -1 +1,12 @@
-This is a paper aiming to cover aspects of social scientific workflow useful for graduate students that are not already well coverd by the other articles in this issue of The Political Methodologist.
+
+This is a paper aiming to cover aspects of social scientific workflow useful for graduate students.
+
+To create a pdf file in RStudio, click on "Knit to PDF". 
+
+At the command line do:
+
+```
+Rscript -e "library(knitr); knit('workflow.Rmd')"
+
+/usr/local/bin/pandoc +RTS -K512m -RTS workflow.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output workflow.pdf --template bowersarticletemplate.latex --number-sections --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --filter /usr/local/bin/pandoc-crossref --bibliography references.bib --filter /usr/local/bin/pandoc-citeproc
+```

bowersarticletemplate.latex

@@ -115,7 +115,7 @@ xetex]{hyperref}
   pdftitle={$title-meta$},
   colorlinks=true,
   linkcolor=BrickRed,
-  citecolor=MidnightBlue,
+  citecolor=blue, %MidnightBlue,
   urlcolor=BrickRed,
   % urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
   % linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
@@ -134,10 +134,13 @@ $endif$
 %\setlength{\parskip}{6pt plus 2pt minus 1pt}
 \usepackage{parskip}
 \setlength{\emergencystretch}{3em}  % prevent overfull lines
-$if(numbersections)$
-$else$
-\setcounter{secnumdepth}{3}
-$endif$
+
+%$if(number_sections)$
+\setcounter{secnumdepth}{5}
+%$else$
+%\setcounter{secnumdepth}{0}
+%$endif$
+
 $if(verbatim-in-note)$
 \VerbatimFootnotes % allows verbatim text in footnotes
 $endif$

references.bib

@@ -1,13 +1,26 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% http://bibdesk.sourceforge.net/
 
-%% Created for Jake Bowers at 2016-06-05 13:55:47 -0400 
+%% Created for Jake Bowers at 2016-06-06 09:16:18 -0400 
 
 
 %% Saved with string encoding Unicode (UTF-8) 
 
 
 
+@misc{norris2015data,
+	Author = {Norris, Pippa},
+	Date-Added = {2016-06-06 13:16:16 +0000},
+	Date-Modified = {2016-06-06 13:16:16 +0000},
+	Howpublished = {https://sites.google.com/site/pippanorris3/research/data#TOC-Democracy-Cross-national-Data-Release-4.0-Fall-2015-New-},
+	Institution = {John F. Kennedy School of Government, Harvard University},
+	Note = {Data file},
+	Title = {Democracy Crossnational Data, Release 4.0},
+	Url = {\url{https://sites.google.com/site/pippanorris3/research/data#TOC-Democracy-Cross-national-Data-Release-4.0-Fall-2015-New-}},
+	Urldate = {Spring 2015},
+	Year = {2015},
+	Bdsk-Url-1 = {http://www.hks.harvard.edu/fs/pnorris/Data/Data.htm}}
+
 @article{gentleman2005reproducible,
 	Author = {Gentleman, Robert},
 	Date-Added = {2016-06-05 17:44:42 +0000},