Before you can open a file, you need to tell R where to find it. You can do this by providing the full path to the file on your system. Be careful to use forward slashes (
\, which you’ll get if you copy file paths in Windows).
filename <- "C:/nexus/matrix.nex"
You can save typing by giving R a working directory. You can think of R as having a file explorer window open invisibly in the background.
You can see the folder that’s open at the moment by typing
getwd() at the console.
setwd() tells R to open a different folder instead.
By setting the directory that your files are in as the working directory, you only need to specify the filename:
setwd("C:/nexus/") # You only need to do this once filename <- "matrix.nex" # Do something with this file # filename <- "tree.nex" # Do something with this file #