Scripting with R

For those more comfortable with R over a terminal, here is an example of an R script that runs AP.exe.

Using R like this, where we run AP.exe with system2 is identical to using a shell; system2 is R's method for running a command.

It is important to still know how to use a shell because you may need to get help (--help) for a command, or construct a command that does something else. Using R is just a wrapper around this process.

It might be helpful to think of R interactive as a shell (like PowerShell or Bash) and RStudio as a terminal.

Just using R to invoke AP.exe adds a lot of complexity. However, you may want to do this if you need to:

  1. to integrate an AP.exe analysis in with the rest of your R analysis
  2. or to batch analyze data.

Example: batching analysis

Almost always you'd want to run AP.exe on more than one file at once. You can use any programming language to do this. Here is an example using R to generate acoustic indices for a folder of audio files:

# Set the directory containing the files
directory <- "C:\\Temp\\Workshop"
# The directory to store the results
base_output_directory <- "C:\\Temp\\Workshop\\BatchIndicesOutput"

# Get a list of audio files inside the directory
# (Get-ChildItem is just like ls, or dir)
files <- list.files(directory, pattern = "*.wav", full.names = TRUE)

# iterate through each file
for(file in files) {
  message("Processing ", file) 
  
  # get just the name of the file
  file_name <- basename(file)
  
  # make a folder for results
  output_directory <- normalizePath(file.path(base_output_directory, file_name))
  dir.create(output_directory, recursive = TRUE)
  
  # prepare command
  command <- sprintf('audio2csv "%s" "Towsey.Acoustic.yml" "%s" ', file, output_directory)
  
  # finally, execute the command
  system2('C:\\AP\\AnalysisPrograms.exe', command)
}

Script explained

Set the directory containing the files

Assign using the left arrow operator <- the folder where the audio files are located to the variable directory , like this:

directory <- "C:\\Temp\\Workshop"

This is the directory we want to look in for files.

Storing the results

Similarly, we choose a directory (base_output_directory) to store the results when the analyses finish, like this:

base_output_directory <- "C:\\Temp\\Workshop\\BatchIndicesOutput"

Listing the audio files inside the directory

Which files do we analyze? We could list them all out by hand - but no one got time for that!

Instead we create a list with all the audio files inside the directory. In this case, we indicated we want all the files with the extension .wav to be listed. If your files have a different extension, you'll need to indicate the right extension after pattern = (and don't forget to put the extension between double quotes)

files <- list.files(directory, pattern = "*.wav", full.names = TRUE)

or, as an example, for FLAC files:

files <- list.files(directory, pattern = "*.flac", full.names = TRUE)

Iterate through each file

The for loop lets us do something for every file we found. In our example, for each file we:

  1. Get the file's name. E.g. From C:\Temp\Workshop\20190801_131213.wav we get 20190801_131213.wav
  2. Create a folder for each result set inside the base_output_directory. The folder will have the name of audio file we're currently working with. E.g. 20190801_131213.wav
  3. Prepare the command, which means put together the bits that will form the command that R and the computer will understand. This is equivalent to typing out the command in a shell.
  4. Finally, use system2 to execute the command and run our analysis. This is equivalent to pressing Enter to run our command in the shell.