Saving your code in a script requires creating a new file that you will need to name.
It might be tempting to name this file `code.R` or `myscript.R`, but you should think a bit harder before choosing a name for your file.
Three important principles for file naming are as follows:
1. File names should be machine readable: Avoid spaces, punctuation, symbols, and accented character. Do not rely on case sensitivity to distinguish files. Make deliberate use of delimiters.
2. File names should be human readable: Use file names that describe what is in the file.
3. File names should play well with default ordering: Start file names with numbers that allow them to be sorted in the order they get used.
Suppose you have the following files in a project folder.
run-first.R
alternative model.R
code for exploratory analysis.R
finalreport.qmd
FinalReport.qmd
fig 1.png
Figure_02.png
model_first_try.R
temp.txt
There are a variety of problems here: the files are misordered, file names contain spaces, there are two files with basically the same name but different capitalization (`finalreport` vs. `FinalReport`), and some file names don't reflect their contents (`run-first` and `temp`).
Below is an alternative way of naming and organizing the same set of files.
01-load-data.R
02-exploratory-analysis.R
03-model-approach-1.R
04-model-approach-2.R
fig-01.png
fig-02.png
notes-on-report-draft.txt
report-2022-03-20.qmd
report-2022-04-02.qmd
Numbering and descriptive names that are similarly formatted allow for a more useful organization of the R scripts.
Additionally, the figures are labelled similarly, the reports are distinguished by dates included in the file names, and `temp` is renamed to `notes-on-report-draft` to better describe its contents.
This will cause you some short-term pain, because now when you restart RStudio, it will no longer remember the results of the code that you ran last time.
But this short-term pain will save you long-term agony because it forces you to capture all important interactions in your code.
There's nothing worse than discovering three months after the fact that you've only stored the results of an important calculation in your workspace, not the calculation itself in your code.
There is a great pair of keyboard shortcuts that will work together to make sure you've captured the important parts of your code in the editor:
1. Press Cmd/Ctrl + Shift + F10 to restart RStudio.
2. Press Cmd/Ctrl + Shift + S to rerun the current script.
I use this pattern hundreds of times a week.
## Where does your analysis live?
R has a powerful notion of the **working directory**.
This is where R looks for files that you ask it to load, and where it will put any files that you ask it to save.
RStudio shows your current working directory at the top of the console:
As a beginning R user, it's OK to let your home directory, documents directory, or any other weird directory on your computer be R's working directory.
But you're six chapters into this book, and you're no longer a rank beginner.
Very soon now you should evolve to organizing your analytical projects into directories and, when working on a project, setting R's working directory to the associated directory.
But you should never do this because there's a better way; a way that also puts you on the path to managing your R work like an expert.
## Paths and directories
Paths and directories are a little complicated because there are two basic styles of paths: Mac/Linux and Windows.
There are three chief ways in which they differ:
1. The most important difference is how you separate the components of the path.
Mac and Linux uses slashes (e.g. `plots/diamonds.pdf`) and Windows uses backslashes (e.g. `plots\diamonds.pdf`).
R can work with either type (no matter what platform you're currently using), but unfortunately, backslashes mean something special to R, and to get a single backslash in the path, you need to type two backslashes!
That makes life frustrating, so I recommend always using the Linux/Mac style with forward slashes.
2. Absolute paths (i.e. paths that point to the same place regardless of your working directory) look different.
In Windows they start with a drive letter (e.g. `C:`) or two backslashes (e.g. `\\servername`) and in Mac/Linux they start with a slash "/" (e.g. `/users/hadley`).
You should **never** use absolute paths in your scripts, because they hinder sharing: no one else will have exactly the same directory configuration as you.
3. The last minor difference is the place that `~` points to.
`~` is a convenient shortcut to your home directory.
Windows doesn't really have the notion of a home directory, so it instead points to your documents directory.
Inspect the folder associated with your project --- notice the `.Rproj` file.
Double-click that file to re-open the project.
Notice you get back to where you left off: it's the same working directory and command history, and all the files you were working on are still open.
Because you followed my instructions above, you will, however, have a completely fresh environment, guaranteeing that you're starting with a clean slate.
In your favorite OS-specific way, search your computer for `diamonds.pdf` and you will find the PDF (no surprise) but *also the script that created it* (`diamonds.R`).
