Filesystems

Pretty much all commonly used operating systems make use of a hierarchically structured filesystem.

This paradigm consists of directories which can contain files and other directories (which can then contain other files and directories and so on).

Absolute vs relative paths

Paths can either be absolute or relative, and the difference is very important. For portability reasons you should almost never use absolute paths.

Absolute path examples

/var/ftp/pub
/etc/samba.smb.conf
/boot/grub/grub.conf

Relative path examples

Sta523/filesystem/
data/access.log
filesystem/nelle/pizza.cfg

Special directories

dir(path = "data/")

[1] "ak"                 "gis"                "lego_sales.rds"    
[4] "movies"             "office_ratings.csv" "phone.csv"         
[7] "pvec_res.Rdata"     "us"                

dir(path = "data/", all.files = TRUE)

 [1] "."                  ".."                 ".DS_Store"         
 [4] "ak"                 "gis"                "lego_sales.rds"    
 [7] "movies"             "office_ratings.csv" "phone.csv"         
[10] "pvec_res.Rdata"     "us"                

Home directory and ~

Tilde (~) is a shortcut that expands to the name of your home directory on unix-like systems.

dir(path = "~/Desktop/Sta523-Sp25/website/")

character(0)

Why ~?

Below is the keyboard from an ADM-3A terminal from the 1970s,

Working directories

R (and OSes) have the concept of a working directory, this is the directory where a program / script is being executed and determines the absolute path of any relative paths used.

getwd()

[1] "/Users/rundel/Desktop/Sta523-Fa25/website/static/slides"

setwd("~/")
getwd()

[1] "/Users/rundel"

RStudio and Working Directories

Just like R, RStudio also makes use of a working directory for each of your sessions - we haven’t had to discuss these yet because when you use an RStudio project, the working directory is automatically set to the directory containing the Rproj file.

Some useful base R filesystem functions

• dir() - list the contents of a directory

• basename() - Removes all of the path up to and include the last path separator (/)

• dirname() - Returns the path up to but excluding the last path separator

• file.path() - a useful alternative to paste0() when combining paths (and urls) as it will add a / when necessary.

• unlink() - delete files and or directories

• dir.create() - create directories

• fs package - collection of filesystem related tools based on unix cli tools (e.g. ls)