good practice

I review a lot of code from students, clients or colleagues and keep giving the same basic recommendations over and over again.
Now I collect important things here so I can easily point to them. Expect this to be expanded :).

source scripts

Before you send someone any code whatsoever, do the following:

  • CTRL+SHIFT+F10 to restart R with a clean workspace. Remember to have the Rstudio settings at Tools - Global Options - General set to: Restore .Rdata into workspace at startup OFF and Save workspace to .RData on exit NEVER
  • copy the script to some other folder than your working place
  • source() the entire script with CTRL+SHIFT+S
  • If something fails, fix it! E.g. stop messing with setwd (see below), copy data files to be read, rename all instances of a renamed object, …
  • Only now send the file (or folder with scripts, data files, etc. as zip file)


  • Use Rstudio projects. They set the wd upon opening and keep projects separate.
  • Never use setwd() because others won’t have that exact path.
    Even you yourself might not, after rearranging folders.
  • Use relative path names, e.g. read.table("datafolder/file.txt") instead of "C:/Users/berry/Desktop/Project/datafolder/file.txt"


Follow the package recommendations in the packages section.


Store the results of long-running computations on disc.
The next time a script is run, they are loaded quickly.

if(  file.exists("objects.Rdata")  )
  load("objects.Rdata") # load previously saved objects
  }  else
  obj1 <-   mean(rnorm(2e7))             # in the first run,
  obj2 <- median(rnorm(2e7))             # compute the objects
  save(obj1, obj2, file="objects.Rdata") # and write them to disc

If you need to rerun an analysis if the last run is older then 6 hours, this could be the condition:

difftime(Sys.time(), file.mtime("objects.Rdata"), units="h") > 6

For a single object, a good alternative to save and load is:

saveRDS(one_single_object, "object.Rdata")
explicit_object_name <- readRDS("object.Rdata")

More on this topic from Rcrastinate