Add bit on naming files + light edits

workflow-scripts.Rmd

@@ -19,12 +19,49 @@ Keep experimenting in the console, but once you have written code that works and
 RStudio will automatically save the contents of the editor when you quit RStudio, and will automatically load it when you re-open.
 Nevertheless, it's a good idea to save your scripts regularly and to back them up.
 
-TODO: Add file naming advice
+## Naming files
+
+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.
 
 ## Running code
 
 The script editor is also a great place to build up complex ggplot2 plots or long sequences of dplyr manipulations.
-The key to using the script editor effectively is to memorise one of the most important keyboard shortcuts: Cmd/Ctrl + Enter.
+The key to using the script editor effectively is to memorize one of the most important keyboard shortcuts: Cmd/Ctrl + Enter.
 This executes the current R expression in the console.
 For example, take the code below.
 If your cursor is at █, pressing Cmd/Ctrl + Enter will run the complete command that generates `not_cancelled`.
@@ -94,7 +131,7 @@ With your R scripts (and your data files), you can recreate the environment.
 It's much harder to recreate your R scripts from your environment!
 You'll either have to retype a lot of code from memory (making mistakes all the way) or you'll have to carefully mine your R history.
 
-To foster this behaviour, I highly recommend that you instruct RStudio not to preserve your workspace between sessions:
+To foster this behavior, I highly recommend that you instruct RStudio not to preserve your workspace between sessions:
 
 ```{r, echo = FALSE, out.width = "75%"}
 knitr::include_graphics("screenshots/rstudio-workspace.png")
@@ -130,7 +167,7 @@ getwd()
 
 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 organising your analytical projects into directories and, when working on a project, setting R's working directory to the associated directory.
+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.
 
 **I do not recommend it**, but you can also set the working directory from within R:
 
@@ -160,7 +197,7 @@ There are three chief ways in which they differ:
 
 ## RStudio projects
 
-R experts keep all the files associated with a project together --- input data, R scripts, analytical results, figures.
+R experts keep all the files associated with a given project together --- input data, R scripts, analytical results, figures.
 This is such a wise and common practice that RStudio has built-in support for this via **projects**.
 
 Let's make a project for you to use while you're working through the rest of this book.
@@ -216,7 +253,7 @@ In summary, RStudio projects give you a solid workflow that will serve you well
 
 -   Create an RStudio project for each data analysis project.
 
--   Keep data files there; we'll talk about loading them into R in \[data import\].
+-   Keep data files there; we'll talk about loading them into R in \@ref(data-import).
 
 -   Keep scripts there; edit them, run them in bits or as a whole.
 
@@ -224,7 +261,7 @@ In summary, RStudio projects give you a solid workflow that will serve you well
 
 -   Only ever use relative paths, not absolute paths.
 
-Everything you need is in one place, and cleanly separated from all the other projects that you are working on.
+Everything you need is in one place and cleanly separated from all the other projects that you are working on.
 
 ## Exercises