I am looking for input on how others organize their R code and output.
My current practice is to write code in blocks in a text file as such:
#================================================= # 19 May 2011 date() # Correlation analysis of variables in sed summary load("/media/working/working_files/R_working/sed_OM_survey.RData") # correlation between estimated surface and mean perc.OM in epi samples cor.test(survey$mean.perc.OM[survey$Depth == "epi"], survey$est.surf.OM[survey$Depth == "epi"])) #==================================================
I then paste the output into another text file, usually with some annotation.
The problems with this method are:
- The code and the output are not explicitly linked other than by date.
- The code and output are organized chronologically and thus can be hard to search.
I have considered making one Sweave document with everything since I could then make a table of contents but this seems like it may be more hassle than the benefits it would provide.
Let me know of any effective routines you have for organizing your R code and output that would allow for efficient searching and editing the analysis.