## All functions

ContinuumRemoval()

Computes continuum removal for matrix shaped data: more efficient than processing individual spectra the convex hull is based on the computation of the derivative between R at a given spectral band and R at the following bands

Write_Big_Image()

write an image which size is > 2**31-1

Write_Image_NativeRes()

write an image resulting from "window processing" at native spatial resolution (assuming square windows & origin at top left corner)

apply_continuum_removal()

prepares data to run multithreaded continuum removal

check_data()

Checks if the data to be processed has the format type expected

compute_FUNCT()

compute functional diversity metrics for an array, given a specific window size

compute_Functional_metrics()

Map functional diversity metrics based on spectral species

compute_NMDS()

computes NMDS

coordPix_kernel()

XXX

create_mask_from_threshold()

create a mask based on NDVI, Green reflectance and NIR reflectance NDVI (min) threshold eliminates non vegetated pixels Blue (max) threshold eliminates Clouds NIR (min) threshold eliminates shadows ! only valid if Optical data!!

diversity_from_plots()

gets alpha diversity indicators from plot

filter_prior_CR()

Filter data prior to continuum removal: - values are expected to be real reflectance values between 0 and 10000 - negative values may occur, so a +100 value is applied to avoid negative - possibly remaining negative values are set to 0 - constant spectra are eliminated

list_shp()

Get list of shapefiles in a directory

map_alpha_div()

maps alpha diversity indicators based on prior selection of PCs

map_beta_div()

maps beta diversity indicator based on spectral species distribution

map_functional_div()

maps functional diversity indicators based on prior selection of PCs

map_spectral_species()

maps spectral species based on PCA file computed previously

minmax()

this function performs rescaling and either defines min and max from each feature in a data set, or applies the transformation based on a previously defined min and max

mnf()

Function to perform MNF

noise()

this function

perform_PCA()

Performs PCA for all images and create PCA file with either all or a selection of PCs

perform_radiometric_filtering()

Performs radiometric filtering based on three criteria: NDVI, NIR reflectance, Blue reflectance

raster2BIL()

converts a raster into BIL format as expected by biodivMapR codes

select_PCA_components()

Check if principal components are properly selected as expected by the method

split_line()

ENVI functions

write_raster()

Writes a matrix or an array into a ENVI BIL raster