Create ScriptingwithR.md

docs/basics/ScriptingwithR.md

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+# Scripting with R
+Since most ecologists and biologists are more used to using R than shell, we provide here an R script to run *AP.exe*
+
+## Set the directory containing the files
+Assing using ``` <- ``` the folder where the audio files are located to the object ``` directory ```, like this:
+
+``` directory <- "C:\\Temp\\Workshop" ```
+
+## Storing the results
+Assign (```<-```) now 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
+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 extenstion between double quotes)
+
+``` files <- list.files(directory, pattern = "*.wav", full.names = TRUE) ```
+
+## Iterate through each file
+Here we indicate we will do this whole process for each file in our list of files:
+1. Get the filename
+2. Create a folder for each file inside the ```base_output_directory```
+3. Prepare the command, which means put together the bits that will form the command that R and the computer will understand
+4. Execute the command - Run the analysis
+
+```
+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)
+}
+```