shell_execution.qmd

# Using R and Python in the shell

## R

Running R in the shell bring slightly different concerns from running R
interactively - which is likely what most R users are used to.

There are a few extra quirks and considerations to running R in the shell, some
of which are listed below.

### Executing scripts

If you are intending to run an R script in the shell, the following line of text
should be at the top of your script:

```sh
#!/usr/bin/env Rscript
```

### Rscript vs R -f

What is the difference?

### Logging methods

Base R's `sink()` function

The `logging` and `logger` packages.

### A note on developing R packages 

When writing functions as part of an R package, it could be useful to keep in 
mind that some users might not be using your package interactively, but through 
the shell.

There is no difference in functionality here, but feedback your package provides,
say through `print()` (discouraged), `message()`/`warning()`/`stop()`, or
`cli::cat_*()` functions, behave slightly differently.