pathdirectories.Rmd

# Paths and directories

* The path of a file/directory is its **location/address** in the file system.

* Your home directory is the one that hosts your personal folder:
	+ for CRG users: **/nfs/users/[yourgroup]/[yourusername]**
  + your **Home** is where your store your data, analysis, etc. You are the only one who can **write** in this folder (apart from the system administrator, if needed).
  
## Tree of directories

<a href="https://sbcrg.github.io/CRG_RIntroduction/images/tree_directories.png"><img src="images/tree_directories.png" alt="rstudio logo" width="1000"/></a>
<br>
<font size="12"> <b>~</b></font>: shortcut to the home directory
<br>
<font size="12"> <b>.</b></font>: current directory
<br>
<font size="12"> <b>..</b></font>: one directory up the tree

In this example, **Rcourse** is a sub-directory of **sbonnin**, which in turn is a sub-direcory of **bi**, and so on.

## Navigate the tree of directory with the R console

* Get the path of the current directory (know where you are working at the moment) with <b>getwd</b> (get working directory):
```{r, eval=FALSE}	
getwd()
```
Hit **Enter/Return** to execute getwd() in the R console.

* Change working directory with **setwd** (set working directory)<br>
(in a Windows or MAC OS system, you would typically **double-click** to reach sub-directories). <br>
Here we use **commands/fonctions** in the **R console**:<br>

Go to a directory giving the **absolute path** (the entire address): 
```{r, eval=FALSE}
setwd("/users/bi/sbonnin/Rcourse")
```

Same as:
```{r, eval=FALSE}
setwd("~/Rcourse")
```

Go to a directory giving the **relative path**. For example, if you are in **Rcourse**, you can either go to **Module1** using the absolute path:
```{r, eval=FALSE}
setwd("/users/bi/sbonnin/Rcourse/Module1")
```
or the relative path:
```{r, eval=FALSE}
setwd("Module1")
```
You are now in: "~/Rcourse/Module1" (check it with getwd() !).
<br>
Move one directory "up" the tree:
```{r, eval=FALSE} 
setwd("..")
```
You are now in: "~/Rcourse"

**HANDS-ON**

1. Execute the following command in the R console:
```{r, eval=FALSE}
setwd("/")
```
2. Where are you now? (use getwd())
3. Find your way back to the **Module1** folder