Although rare, there are some cases where a single R script contains the totality of your research/analyses. This may happen if you are doing simulation studies, for example. For most cases, an analysis will consist of a script (or scripts), and at least one data set. I refer to any R analysis that uses at least two files as an R project.
In R projects, special attention must be paid to how the files are stored relative to each other. For example, if we stored the file SAT_Scores_NYC_2010.csv on our desktop, the data import line would have read:
read.csv("/Users/bensisko/Desktop/SAT_Scores_NYC_2010.csv") If you want to send this analysis to a contributor to be replicated, we would send them the script and the data file. Even if we instructed them to place the file on their desktop, the script would still not be reproducible. Our collaborators on Windows and Unix would have to manually change the argument of read.csv to C:/Users/jameskirk/Desktop/SAT_Scores_NYC_2010.csv, or /home...
