Extracting reflectance data from SpectraSuite JCAMP files in R

May 6, 2011

(This article was first published on PlanetFlux, and kindly contributed to R-bloggers)

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:

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