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Spectral diversity in Hill numbers

geo_spectral_diversity.Rd

geo_spectral_diversity() maps diversity from satellite or drone imagery with the same Hill numbers used for species (Jost 2006), so spectral and field diversity are on one scale. Following the spectral species approach (Féret and Asner 2014):

  1. the bands are standardised and reduced with principal components (keeping the components that explain pca_var of the variance);

  2. pixels are grouped into k spectral species by k-means;

  3. in a moving window around each pixel, the spectral species are counted and their Hill numbers of order q computed (q = 0: number of spectral species; 1: exponential Shannon; 2: inverse Simpson).

The window step runs in C++ on several cores.

Usage

geo_spectral_diversity(
  x,
  window = 5,
  k = 20,
  q = c(0, 1, 2),
  pca_var = 0.95,
  min_cells = NULL,
  sample = 20000
)

Arguments

x

A multi-band SpatRaster or file path.

window

Window size in cells (odd; 5 means 5 x 5).

k

Number of spectral species.

q

Orders of diversity.

pca_var

Share of variance the principal components must keep.

min_cells

Minimum valid cells in a window; fewer gives NA.

sample

Number of pixels used to fit the PCA and k-means (all pixels are then classified).

Value

A SpatRaster with layers q0, q1, q2 (one per q) and spectral_species; attribute "spectral" holds the PCA variance kept, number of components and the k-means centres.

References

Féret, J.-B. and Asner, G. P. (2014). Mapping tropical forest canopy diversity using high-fidelity imaging spectroscopy. Ecological Applications, 24, 1289-1296. doi:10.1890/13-1824.1

Jost, L. (2006). Entropy and diversity. Oikos, 113, 363-375. doi:10.1111/j.2006.0030-1299.14714.x

Examples

s2 <- terra::rast(system.file("ex/sent2_L2A_2024-08-24.tif", package = "terra"))
set.seed(1)
sd <- geo_spectral_diversity(s2, window = 5, k = 15)
sd
#> class       : SpatRaster
#> size        : 90, 95, 4  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 5.741667, 6.533333, 49.44167, 50.19167  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source(s)   : memory
#> varnames    : sent2_L2A_2024-08-24
#>               sent2_L2A_2024-08-24
#>               sent2_L2A_2024-08-24
#>               sent2_L2A_2024-08-24
#> names       : q0,        q1,        q2, spectral_species
#> min values  :  2,  1.735126,  1.555556,                1
#> max values  : 14, 12.493226, 11.363636,               15
attr(sd, "spectral")$components
#> [1] 2