Is there a quick way on Mac to put thousands of files from different folders into one folder or is there a way for R to read thousands of files in different working directories simultaneously?
Some relevant details are missing from your question (e.g. file format, whether all the subfolders are in the same main folder). However, you may wanna look over two functions:
list.files()
combined to
lapply()
When reading the files are a good place to start. Please provide more details so we can help you in a better way.