The command setwd("~/") should set your working directory to your home directory. You might be experiencing problems because the OS you are using does not recognise "~/" as your home directory: this might be because of the OS, or it might be because of not having set that as your home directory elsewhere.
As you have tagged the post using RStudio:
- In the bottom right window move the tab over to ‘files’.
- Navigate through there to whichever folder you were planning to use as your working directory.
- Under ‘more’ click ‘set as working directory’
You will now have set the folder as your working directory. Use the command getwd() to get the working directory as it is now set, and save that as a variable string at the top of your script. Then use setwd with that string as the argument, so that each time you run the script you use the same directory.
For example at the top of my script I would have:
work_dir <- "C:/Users/john.smith/Documents" setwd(work_dir)