Things are not that gory with knitr. You only need to use the option cache=TRUE and it will take care of most of the things you mentioned. For example, objects in a chunk are automatically saved and lazy loaded; when code is modified, old cache will be automatically removed and new cache will be built.
You can take a look at the Cache section in the manual: https://github.com/downloads/yihui/knitr/knitr-manual.pdf And more explanations for using cache safely here: http://yihui.name/knitr/demo/cache/ Regards, Yihui -- Yihui Xie <xieyi...@gmail.com> Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Thu, Apr 5, 2012 at 12:47 PM, Alexander Shenkin <ashen...@ufl.edu> wrote: > Reproducibility is important, and as I mentioned in a previous email, > there are probably ways I could avoid running the entire script over and > over again with each sweave compilation. Still, relying on saved > workspaces, temporary files or caches still has some of the issues that > working in the main environment does. Specifically, you're not working > with the base data all the way through the final analyses each time you > run the sweave doc. To produce those workspace, files or caches > requires a run of scripts. If those scripts have changed, or if your > data have changed, then your workspace, files and/or cache is then just > as out of date as your workspace. Saving workspaces, files and/or > caches still requires care that they're not saved after having been > modified by the command line, etc. I think that working with saved > workspaces, files and/or caches is probably less prone to "pollution" > than working in the main environment, but it's far from failsafe. > > As long as the final sweave doc is run with scripts from beginning to > end, getting the sweave doc up to snuff by working more quickly in the > main environment is acceptable IMHO. So is working with the other > methods above. > > Best, > Allie > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
