I've been using an OceanOptics USB4000 spectrometer in research on biomass accumulation and climate in South Africa.
This post presents a R function that will read in JCAMP files from the SpectraSuite software and output a vector of reflectance values. SpectraSuite can convert binary output files to JCAMP files if they weren't saved as JCAMP.
You can use this to process a folder of spectra and return a data frame with a column for each file as follows:
And here's another function that will calculate NDVI similar to several satellite products:
You can apply this to the output of spectracompile() like this:
Here's a few random spectra from various fynbos species: