I did a little roundup of some R workflow/analysis writeups on my blog a few weeks ago
Brian Fannin's represtools 
(a ~portmanteau of reproducible research tools) might be of particular interest. Also, the recent PeerJ preprint, Packaging data analytical work reproducibly using R (and friends) by Ben Marwick, Carl Boettiger, and Lincoln Mullen (which I don't think was in that roundup post) is 
!