On Thu, May 3, 2012 at 1:53 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > "I like the idea of staying with absolute paths." > > Before you write too much R code that builds in absolute paths, please > consider how difficult it will be to adjust all of those paths if you need to > run on a different computer or you need to reorganize your overall directory > structure. If you keep related R files in the same project directory, you can > collapse all of those paths down to short relative paths, and do one setwd at > the beginning, or learn to manually set your base working directory as a > matter of habit before each working session. (This habit is useful in more > areas than just R programming.)
I agree with this, which is why I suggested you use absolute paths *until you get more comfortable with the file system.* It's a good way to diagnose your problem and figure out how to deal with paths on Linux, but not a good long-term strategy unless you expect that you will never ever move anything or change to a new computer. An intermediate solution that I use a lot is to put something like this at the beginning of R script file: basepath = "/home/sarahg/whatever" and then load files using something like read.table(paste(basepath, "plantdata.csv", sep="/")) This eases portability between computers: I exchange a lot of analyses with postdocs, students and techs, and somehow they've not all become convinced that my way of organizing directories is the best one. Using an object with the absolute path for the data means that we can pass things back and forth with only changing one value within the script rather than all input/output commands. Sarah -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ 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.
