KS function updates - vpr_autoid_copy

[EOGrady21]

Comparative analysis of vpr_autoid_copy and vpr_autoid_copy_th (provided locally by @kevinsorochan ) shows following major difference:

• reads in CNN output files to get probability values with each classification
• only copies images where probability is less than 0.9 (! HARDCODED!) threshold

Suggestions for integration into vprr::vpr_autoid_copy()

• [x] add argument for cnn output files (optional)

• [x] add argument for threshold (optional)

These updates will allow KS functionality within the existing package function structure, while also being backwards compatible with other workflows which are not utilizing this cnn/ threshold method.

[EOGrady21]

I made a discovery in my own workflow to speed up image copying, I'm going to add it to this list of updates to be made...

using fs::file.copy() is much much faster than our previous method (~20 minutes to copy an entire cruise of images)

see numeric comparison here: https://stackoverflow.com/questions/49888078/copying-files-over-the-network-is-much-slower-with-file-copy-than-systemmv

[EOGrady21]

This update should improve the copying workflow significantly. It is worth noting that speed will be increased if files are being copied to and from on an internal computer drive (rather than copying from an external drive - which will limit transfer rates based on USB capabilities)